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Sample records for large globular protein

  1. Aeolotopic interactions of globular proteins

    PubMed Central

    Lomakin, Aleksey; Asherie, Neer; Benedek, George B.

    1999-01-01

    Protein crystallization, aggregation, liquid–liquid phase separation, and self-assembly are important in protein structure determination in the industrial processing of proteins and in the inhibition of protein condensation diseases. To fully describe such phase transformations in globular protein solutions, it is necessary to account for the strong spatial variation of the interactions on the protein surface. One difficulty is that each globular protein has its own unique surface, which is crucial for its biological function. However, the similarities amongst the macroscopic properties of different protein solutions suggest that there may exist a generic model that is capable of describing the nonuniform interactions between globular proteins. In this paper we present such a model, which includes the short-range interactions that vary from place to place on the surface of the protein. We show that this aeolotopic model [from the Greek aiolos (“variable”) and topos (“place”)] describes the phase diagram of globular proteins and provides insight into protein aggregation and crystallization. PMID:10449715

  2. Nonlinear dynamics of globular proteins

    SciTech Connect

    Lomdahl, P.S.

    1983-01-01

    Some ongoing work aimed at generalizing DAVYDOV's ideas to a real globular protein is described. So far, a computer code, GLOP, which calculates amide-I bond energy evolution on a globular protein has been developed and tested. The code is quite versatile and takes as input the coordinates of a protein. The full geometry of the molecule is then taken into account when the dipole-dipole interaction between peptide groups is calculated. The amide-I energy is coupled to one intramolecular excitation, but can without difficulty be extended to more or to include intermolecular excitations.

  3. Models of globular proteins in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Wentzel, Nathaniel James

    Protein crystallization is a continuing area of research. Currently, there is no universal theory for the conditions required to crystallize proteins. A better understanding of protein crystallization will be helpful in determining protein structure and preventing and treating certain diseases. In this thesis, we will extend the understanding of globular proteins in aqueous solutions by analyzing various models for protein interactions. Experiments have shown that the liquid-liquid phase separation curves for lysozyme in solution with salt depend on salt type and salt concentration. We analyze a simple square well model for this system whose well depth depends on salt type and salt concentration, to determine the phase coexistence surfaces from experimental data. The surfaces, calculated from a single Monte Carlo simulation and a simple scaling argument, are shown as a function of temperature, salt concentration and protein concentration for two typical salts. Urate Oxidase from Asperigillus flavus is a protein used for studying the effects of polymers on the crystallization of large proteins. Experiments have determined some aspects of the phase diagram. We use Monte Carlo techniques and perturbation theory to predict the phase diagram for a model of urate oxidase in solution with PEG. The model used includes an electrostatic interaction, van der Waals attraction, and a polymerinduced depletion interaction. The results agree quantitatively with experiments. Anisotropy plays a role in globular protein interactions, including the formation of hemoglobin fibers in sickle cell disease. Also, the solvent conditions have been shown to play a strong role in the phase behavior of some aqueous protein solutions. Each has previously been treated separately in theoretical studies. Here we propose and analyze a simple, combined model that treats both anisotropy and solvent effects. We find that this model qualitatively explains some phase behavior, including the existence of

  4. Large scale structure of the globular cluster population in Coma

    NASA Astrophysics Data System (ADS)

    Gagliano, Alexander T.; O'Neill, Conor; Madrid, Juan P.

    2016-01-01

    A search for globular cluster candidates in the Coma Cluster was carried out using Hubble Space Telescope data taken with the Advanced Camera for Surveys. We combine different observing programs including the Coma Treasury Survey in order to obtain the large scale distribution of globular clusters in Coma. Globular cluster candidates were selected through careful morphological inspection and a detailed analysis of their magnitude and colors in the two available wavebands, F475W (Sloan g) and F814W (I). Color Magnitude Diagrams, radial density plots and density maps were then created to characterize the globular cluster population in Coma. Preliminary results show the structure of the intergalactic globular cluster system throughout Coma, among the largest globular clusters catalogues to date. The spatial distribution of globular clusters shows clear overdensities, or bridges, between Coma galaxies. It also becomes evident that galaxies of similar luminosity have vastly different numbers of associated globular clusters.

  5. Critical examination of the colloidal particle model of globular proteins.

    PubMed

    Sarangapani, Prasad S; Hudson, Steven D; Jones, Ronald L; Douglas, Jack F; Pathak, Jai A

    2015-02-03

    Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes

  6. Critical Examination of the Colloidal Particle Model of Globular Proteins

    PubMed Central

    Sarangapani, Prasad S.; Hudson, Steven D.; Jones, Ronald L.; Douglas, Jack F.; Pathak, Jai A.

    2015-01-01

    Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes

  7. Detection of disordered regions in globular proteins using ¹³C-detected NMR.

    PubMed

    Gray, Felicia L V; Murai, Marcelo J; Grembecka, Jolanta; Cierpicki, Tomasz

    2012-12-01

    Characterization of disordered regions in globular proteins constitutes a significant challenge. Here, we report an approach based on ¹³C-detected nuclear magnetic resonance experiments for the identification and assignment of disordered regions in large proteins. Using this method, we demonstrate that disordered fragments can be accurately identified in two homologs of menin, a globular protein with a molecular weight over 50 kDa. Our work provides an efficient way to characterize disordered fragments in globular proteins for structural biology applications.

  8. Thermodynamics of the temperature-induced unfolding of globular proteins.

    PubMed Central

    Khechinashvili, N. N.; Janin, J.; Rodier, F.

    1995-01-01

    The heat capacity, enthalpy, entropy, and Gibbs energy changes for the temperature-induced unfolding of 11 globular proteins of known three-dimensional structure have been obtained by microcalorimetric measurements. Their experimental values are compared to those we calculate from the change in solvent-accessible surface area between the native proteins and the extended polypeptide chain. We use proportionality coefficients for the transfer (hydration) of aliphatic, aromatic, and polar groups from gas phase to aqueous solution, we estimate vibrational effects, and we discuss the temperature dependence of each constituent of the thermodynamic functions. At 25 degrees C, stabilization of the native state of a globular protein is largely due to two favorable terms: the entropy of non-polar group hydration and the enthalpy of interactions within the protein. They compensate the unfavorable entropy change associated with these interactions (conformational entropy) and with vibrational effects. Due to the large heat capacity of nonpolar group hydration, its stabilizing contribution decreases quickly at higher temperatures, and the two unfavorable entropy terms take over, leading to temperature-induced unfolding. PMID:7670374

  9. Universality of vibrational spectra of globular proteins

    NASA Astrophysics Data System (ADS)

    Na, Hyuntae; Song, Guang; ben-Avraham, Daniel

    2016-02-01

    It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e. regardless of the protein in question, it closely follows one universal curve. The present study, including 135 proteins analyzed with a full atomic empirical potential (CHARMM22) and using the full complement of all atoms Cartesian degrees of freedom, goes far beyond previous claims of universality, confirming that universality holds even in the frequency range that is well above 100 cm-1 (300-4000 cm-1), where peaks and turns in the density of states are faithfully reproduced from one protein to the next. We also characterize fluctuations of the spectral density from the average, paving the way to a meaningful discussion of rare, unusual spectra and the structural reasons for the deviations in such ‘outlier’ proteins. Since the method used for the derivation of the vibrational modes (potential energy formulation, set of degrees of freedom employed, etc) has a dramatic effect on the spectral density, another significant implication of our findings is that the universality can provide an exquisite tool for assessing and improving the quality of potential functions and the quality of various models used for NMA computations. Finally, we show that the input configuration also affects the density of modes, thus emphasizing the importance of simplified potential energy formulations that are minimized at the outset. In summary, our findings call for a serious two-way dialogue between theory and experiment: experimental spectra of proteins could now guide the fine tuning of theoretical empirical potentials, and the various features and peaks observed in theoretical studies—being universal, and hence now rising in importance—would hopefully spur experimental confirmation.

  10. Variable stars in large Magellanic cloud globular clusters. III. Reticulum

    SciTech Connect

    Kuehn, Charles A.; Dame, Kyra; Smith, Horace A.; De Lee, Nathan E-mail: damekyra@msu.edu E-mail: nathan.delee@vanderbilt.edu; and others

    2013-06-01

    This is the third in a series of papers studying the variable stars in old globular clusters in the Large Magellanic Cloud. The primary goal of this series is to look at how the characteristics and behavior of RR Lyrae stars in Oosterhoff-intermediate systems compare to those of their counterparts in Oosterhoff-I/II systems. In this paper we present the results of our new time-series BVI photometric study of the globular cluster Reticulum. We found a total of 32 variables stars (22 RRab, 4 RRc, and 6 RRd stars) in our field of view. We present photometric parameters and light curves for these stars. We also present physical properties, derived from Fourier analysis of light curves, for some of the RR Lyrae stars. We discuss the Oosterhoff classification of Reticulum and use our results to re-derive the distance modulus and age of the cluster.

  11. Drug-Mediated Laser Photo Damage of Globular Proteins

    DTIC Science & Technology

    2009-03-10

    sulfonatophenyl-porphyrin (TPPS)) with two globular proteins ( -lactoglobulin ( BLG ) and tubulin) and the effect that the irradiation of the...porphyrins produce on the conformation of the two proteins. We established that both porphyrin can bind the proteins. However while PPIX binding to BLG is...binding by itself does not produce conformational changes in the proteins but that, in the case of BLG , TPPS increases the stability of the protein to

  12. Binding of globular proteins to DNA from surface tension measurement.

    PubMed

    Mitra, A; Chattoraj, D K; Chakraborty, P

    2001-10-01

    Extent of binding (gammap) of globular proteins to calf-thymus DNA have been measured in mole per mole of nucleotide as function of equilibrium protein concentration. We have exploited measurement of the surface tension of the protein solution in the presence and absence of DNA to calculate the binding ration (gammap). Interaction of bovine serum albumin with DNA has been studied at different pH. Interaction of bovine serum albumin with DNA has been studied at different pH, ionic strength and in presence of Ca2+. Interaction of BSA with denatured DNA has also been investigated. Binding isotherms for other globular proteins like beta-lactoglobulin, alpha-lactalbumin and lysozyme have been compared under identical physicochemical condition. It has been noted with considerable interest that globular form of protein is important to some extent in protein-DNA interaction. An attempt has been made to explain the significance of difference in binding ratios of these two biopolymers in aqueous medium for different systems in the light of electrostatic and hydrophobic effects. Values of maximum binding ration (gammap(m)) at saturated level for different systems have been also presented. The Gibb's free energy decrease (-deltaG0) of the binding of proteins to DNA has been compared more precisely for the saturation of binding sites in the DNA with the change of activity of protein in solution from zero to unity in the rational mole fraction scale.

  13. Discrete structure of van der Waals domains in globular proteins.

    PubMed

    Berezovsky, Igor N

    2003-03-01

    Most globular proteins are divisible by domains, distinct substructures of the globule. The notion of hierarchy of the domains was introduced earlier via van der Waals energy profiles that allow one to subdivide the proteins into domains (subdomains). The question remains open as to what is the possible structural connection of the energy profiles. The recent discovery of the loop-n-lock elements in the globular proteins suggests such a structural connection. A direct comparison of the segmentation by van der Waals energy criteria with the maps of the locked loops of nearly standard size reveals a striking correlation: domains in general appear to consist of one to several such loops. In addition, it was demonstrated that a variety of subdivisions of the same protein into domains is just a regrouping of the loop-n-lock elements.

  14. Variable Stars in Large Magellanic Cloud Globular Clusters. III. Reticulum

    NASA Astrophysics Data System (ADS)

    Kuehn, Charles A.; Dame, Kyra; Smith, Horace A.; Catelan, Márcio; Jeon, Young-Beom; Nemec, James M.; Walker, Alistair R.; Kunder, Andrea; Pritzl, Barton J.; De Lee, Nathan; Borissova, Jura

    2013-06-01

    This is the third in a series of papers studying the variable stars in old globular clusters in the Large Magellanic Cloud. The primary goal of this series is to look at how the characteristics and behavior of RR Lyrae stars in Oosterhoff-intermediate systems compare to those of their counterparts in Oosterhoff-I/II systems. In this paper we present the results of our new time-series BVI photometric study of the globular cluster Reticulum. We found a total of 32 variables stars (22 RRab, 4 RRc, and 6 RRd stars) in our field of view. We present photometric parameters and light curves for these stars. We also present physical properties, derived from Fourier analysis of light curves, for some of the RR Lyrae stars. We discuss the Oosterhoff classification of Reticulum and use our results to re-derive the distance modulus and age of the cluster. Based on observations taken with the SMARTS 1.3 m telescope operated by the SMARTS Consortium and observations taken at the Southern Astrophysical Research (SOAR) telescope, which is a joint project of the Ministério da Ciência, Tecnologia, e Inovação (MCTI) da República Federativa do Brasil, the U.S. National Optical Astronomy Observatory (NOAO), the University of North Carolina at Chapel Hill (UNC), and Michigan State University (MSU).

  15. Molecular weight characterization of single globular proteins using optical nanotweezers.

    PubMed

    Wheaton, Skyler; Gordon, Reuven

    2015-07-21

    We trap a set of molecular weight standard globular proteins using a double nanohole optical trap. The root mean squared variation of the trapping laser transmission intensity gives a linear dependence with the molecular weight, showing the potential for analysis of globular proteins. The characteristic time of the autocorrelation of the trapping laser intensity variations scales with a -2/3 power dependence with the volume of the particle. A hydrodynamic laser tweezer model is used to explain these dependencies. Since this is a single particle technique that operates in solution and can be used to isolate an individual particle, we believe that it provides an interesting alternative to existing analysis methods and shows promise to expand the capabilities of protein related studies to the single particle level.

  16. Dynamic Prestress in a Globular Protein

    PubMed Central

    Edwards, Scott A.; Wagner, Johannes; Gräter, Frauke

    2012-01-01

    A protein at equilibrium is commonly thought of as a fully relaxed structure, with the intra-molecular interactions showing fluctuations around their energy minimum. In contrast, here we find direct evidence for a protein as a molecular tensegrity structure, comprising a balance of tensed and compressed interactions, a concept that has been put forward for macroscopic structures. We quantified the distribution of inter-residue prestress in ubiquitin and immunoglobulin from all-atom molecular dynamics simulations. The network of highly fluctuating yet significant inter-residue forces in proteins is a consequence of the intrinsic frustration of a protein when sampling its rugged energy landscape. In beta sheets, this balance of forces is found to compress the intra-strand hydrogen bonds. We estimate that the observed magnitude of this pre-compression is enough to induce significant changes in the hydrogen bond lifetimes; thus, prestress, which can be as high as a few 100 pN, can be considered a key factor in determining the unfolding kinetics and pathway of proteins under force. Strong pre-tension in certain salt bridges on the other hand is connected to the thermodynamic stability of ubiquitin. Effective force profiles between some side-chains reveal the signature of multiple, distinct conformational states, and such static disorder could be one factor explaining the growing body of experiments revealing non-exponential unfolding kinetics of proteins. The design of prestress distributions in engineering proteins promises to be a new tool for tailoring the mechanical properties of made-to-order nanomaterials. PMID:22589712

  17. Role of solvent for globular proteins in solution.

    PubMed

    Shiryayev, Andrey; Pagan, Daniel L; Gunton, James D; Rhen, D S; Saxena, Avadh; Lookman, Turab

    2005-06-15

    The properties of the solvent affect the behavior of the solution. We propose a model that accounts for the contribution of the solvent free energy to the free energy of globular proteins in solution. For the case of an attractive square-well potential, we obtain an exact mapping of the phase diagram of this model without solvent to the model that includes the solute-solvent contribution. In particular we find for appropriate choices of parameters upper critical points, lower critical points, and even closed loops with both upper and lower critical points similar to those found before [Macromolecules 36, 5843 (2003)]. In the general case of systems whose interactions are not attractive square wells, this mapping procedure can be a first approximation to understand the phase diagram in the presence of solvent. We also present simulation results for both the square-well model and a modified Lennard-Jones model.

  18. Effect of ethanol on structures and interactions among globular proteins

    NASA Astrophysics Data System (ADS)

    Kundu, Sarathi; Aswal, V. K.; Kohlbrecher, J.

    2017-02-01

    Structures and interactions among globular proteins BSA and lysozyme are explored by small angle neutron scattering (SANS) technique at pD ≈ 7.0 by varying ethanol concentration. Interaction behaviours are also obtained in presence of monovalent salt (NaCl). SANS analysis shows that for both lower and higher BSA concentrations and in presence of NaCl, combination of intermediate-range repulsion and weak long-range attraction is responsible for the effective interaction behaviours with the variation of ethanol concentration. For lysozyme, interaction nature is same as BSA in absence of NaCl but in presence of NaCl, fractal structure factor explains the interaction behaviours.

  19. Universal convergence of the specific volume changes of globular proteins upon unfolding.

    PubMed

    Schweiker, Katrina L; Fitz, Victoria W; Makhatadze, George I

    2009-11-24

    Both pressure and temperature are important environmental variables, and to obtain a complete understanding of the mechanisms of protein folding, it is necessary to determine how protein stability is dependent on these fundamental thermodynamic parameters. Although the temperature dependence of protein stability has been widely explored, the dependence of protein stability on pressure is not as well studied. In this paper, we report the results of the direct thermodynamic determination of the change in specific volume (DeltaV/V) upon protein unfolding, which defines the pressure dependence of protein stability, for five model proteins (ubiquitin, eglin c, ribonuclease A, lysozyme, and cytochrome c). We have shown that the specific volumetric changes upon unfolding for four of the proteins (ubiquitin, eglin c, ribonuclease A, and lysozyme) appear to converge to a common value at high temperatures. Analysis of various contributions to the change in volume upon protein unfolding allowed us to put forth the hypothesis that the change in volume due to hydration is very close to zero at this temperature, such that DeltaV/V is defined largely by the total volume of cavities and voids within a protein, and that this is a universal property of all small globular proteins without prosthetic groups. To test this hypothesis, additional experiments were performed with variants of eglin c that had site-directed substitutions at two buried positions, to create an additional cavity in the protein core. The results of these experiments, coupled with the structural analysis of cytochrome c showing a lower packing density compared to those of the other four proteins, provided further support for the hypothesis. Finally, we have shown that the deviation of the high-temperature DeltaV value of a given protein from the convergence value can be used to determine the size of the excess cavities in globular proteins.

  20. General Trends of Dihedral Conformational Transitions in a Globular Protein

    PubMed Central

    Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew

    2017-01-01

    Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and Adaptive Biasing Force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions ~2 times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the Bend, Coil and Turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein sidechains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Sidechains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. PMID:26799251

  1. General trends of dihedral conformational transitions in a globular protein.

    PubMed

    Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C; McCammon, J Andrew

    2016-04-01

    Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.

  2. Lipases at interfaces: unique interfacial properties as globular proteins.

    PubMed

    Reis, P; Miller, R; Krägel, J; Leser, M; Fainerman, V B; Watzke, H; Holmberg, K

    2008-06-01

    The adsorption behavior of two globular proteins, lipase from Rhizomucor miehei and beta-lactoglobulin, at inert oil/water and air/water interfaces was studied by the pendant drop technique. The kinetics and adsorption isotherms were interpreted for both proteins in different environments. It was found that the adopted mathematical models well describe the adsorption behavior of the proteins at the studied interfaces. One of the main findings is that unique interfacial properties were observed for lipase as compared to the reference beta-lactoglobulin. A folded drop with a "skinlike" film was formed for the two proteins after aging followed by compression. This behavior is normally associated with protein unfolding and covalent cross-linking at the interface. Despite this, the lipase activity was not suppressed. By highlighting the unique interfacial properties of lipases, we believe that the presented work contributes to a better understanding of lipase interfacial activation and the mechanisms regulating lipolysis. The results indicate that the understanding of the physical properties of lipases can lead to novel approaches to regulate their activity.

  3. General trends of dihedral conformational transitions in a globular protein

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew

    2016-02-15

    In this paper, dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. In conclusion, these general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.

  4. General trends of dihedral conformational transitions in a globular protein

    DOE PAGES

    Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; ...

    2016-02-15

    In this paper, dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed bymore » the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. In conclusion, these general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.« less

  5. De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

    PubMed Central

    Kosciolek, Tomasz; Jones, David T.

    2014-01-01

    The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm – FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical potentials or contacts alone. Results show up to nearly 80% of correct predictions (TM-score ≥0.5) within analysed dataset and a mean TM-score of 0.54. Unsuccessful modelling cases emerged either from conformational sampling problems, or insufficient contact prediction accuracy. Nevertheless, a strong dependency of the quality of final models on the fraction of satisfied predicted long-range contacts was observed. This not only highlights the importance of these contacts on determining the protein fold, but also (combined with other ensemble-derived qualities) provides a powerful guide as to the choice of correct models and the global quality of the selected model. A proposed quality assessment scoring function achieves 0.93 precision and 0.77 recall for the discrimination of correct folds on our dataset of decoys. These findings suggest the approach is well-suited for blind predictions on a variety of globular proteins of unknown 3D structure, provided that enough homologous sequences are available to construct a large and accurate multiple sequence alignment for the initial contact prediction step. PMID:24637808

  6. De novo structure prediction of globular proteins aided by sequence variation-derived contacts.

    PubMed

    Kosciolek, Tomasz; Jones, David T

    2014-01-01

    The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm--FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical potentials or contacts alone. Results show up to nearly 80% of correct predictions (TM-score ≥0.5) within analysed dataset and a mean TM-score of 0.54. Unsuccessful modelling cases emerged either from conformational sampling problems, or insufficient contact prediction accuracy. Nevertheless, a strong dependency of the quality of final models on the fraction of satisfied predicted long-range contacts was observed. This not only highlights the importance of these contacts on determining the protein fold, but also (combined with other ensemble-derived qualities) provides a powerful guide as to the choice of correct models and the global quality of the selected model. A proposed quality assessment scoring function achieves 0.93 precision and 0.77 recall for the discrimination of correct folds on our dataset of decoys. These findings suggest the approach is well-suited for blind predictions on a variety of globular proteins of unknown 3D structure, provided that enough homologous sequences are available to construct a large and accurate multiple sequence alignment for the initial contact prediction step.

  7. Globular-disorder transition in proteins: a compromise between hydrophobic and electrostatic interactions?

    PubMed

    Baruah, Anupaul; Biswas, Parbati

    2016-08-17

    The charge-hydrophobicity correlation of globular and disordered proteins is explored using a generalized self-consistent field theoretical method combined with Monte Carlo simulations. Globular and disordered protein sequences with varied mean net charge and mean hydrophobicity are designed by theory, while Metropolis Monte Carlo generates a suitable ensemble of conformations. Results imply a transition of the dominant interactions between globular and disordered proteins across the charge-hydrophobicity boundary. It is observed that the charge-hydrophobicity boundary actually represents a trade-off between the repulsive and attractive interactions in a protein sequence. The attractive interactions predominate on the globular side of the boundary, while the repulsive interactions prevail on the disordered side. For globular proteins, core forming hydrophobic interactions are dominant leading to a minimally frustrated native conformation. For disordered proteins, the repulsive electrostatic interactions prevail yielding a minimally frustrated region comprising of an expanded, dynamic conformational ensemble. Thus, protein disorder, like protein folding, satisfies the principle of minimal frustration. All results are compared to real globular and disordered proteins. Thus this algorithm may be useful to probe the conformational characteristics of disordered proteins.

  8. The kinematics of globular clusters in the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Freeman, K. C.; Illingworth, G.; Oemler, A., Jr.

    1983-09-01

    Velocities have been determined for 35 globular clusters in the LMC. These data have been combined with data from other sources to give velocities for 59 clusters ranging in age from ≡108 to ≡1010 yr. Clusters younger than ≡109 yr form a flattened system having a low line-of-sight velocity dispersion (≡15 km s-1), an amplitude for their rotation of 37±5 km s-1, a galactocentric systemic velocity of 40±3 km s-1, and a line of nodes in position angle 1°±5°. The older clusters are also flattened to a disklike system with an intrinsic line-of-sight dispersion of only 17 km s-1, and a rotation amplitude of 41±4 km s-1. Surprisingly both the systemic velocity at 26±2 km s-1, and the position angle of the line of nodes at 41°±5 are very significantly different for these older clusters. This enigmatic situation resisted all attempts at a solution. The data for the oldest clusters suggest that there is no evidence for a kinematic halo population among the globular clusters in the LMC.

  9. Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation.

    PubMed

    Yoneda, Juliana Sakamoto; Miles, Andew J; Araujo, Ana Paula Ulian; Wallace, B A

    2017-04-01

    Globular proteins composed of different secondary structures and fold types were examined by synchrotron radiation circular dichroism spectroscopy to determine the effects of dehydration on their secondary structures. They exhibited only minor changes upon removal of bulk water during film formation, contrary to previously reported studies of proteins dehydrated by lyophilization (where substantial loss of helical structure and gain in sheet structure was detected). This near lack of conformational change observed for globular proteins contrasts with intrinsically disordered proteins (IDPs) dried in the same manner: the IDPs, which have almost completely unordered structures in solution, exhibited increased amounts of regular (mostly helical) secondary structures when dehydrated, suggesting formation of new intra-protein hydrogen bonds replacing solvent-protein hydrogen bonds, in a process which may mimic interactions that occur when IDPs bind to partner molecules. This study has thus shown that the secondary structures of globular and intrinsically disordered proteins behave very differently upon dehydration, and that films are a potentially useful format for examining dehydrated soluble proteins and assessing IDPs structures.

  10. Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation

    PubMed Central

    Yoneda, Juliana Sakamoto; Miles, Andew J.; Araujo, Ana Paula Ulian

    2017-01-01

    Abstract Globular proteins composed of different secondary structures and fold types were examined by synchrotron radiation circular dichroism spectroscopy to determine the effects of dehydration on their secondary structures. They exhibited only minor changes upon removal of bulk water during film formation, contrary to previously reported studies of proteins dehydrated by lyophilization (where substantial loss of helical structure and gain in sheet structure was detected). This near lack of conformational change observed for globular proteins contrasts with intrinsically disordered proteins (IDPs) dried in the same manner: the IDPs, which have almost completely unordered structures in solution, exhibited increased amounts of regular (mostly helical) secondary structures when dehydrated, suggesting formation of new intra‐protein hydrogen bonds replacing solvent‐protein hydrogen bonds, in a process which may mimic interactions that occur when IDPs bind to partner molecules. This study has thus shown that the secondary structures of globular and intrinsically disordered proteins behave very differently upon dehydration, and that films are a potentially useful format for examining dehydrated soluble proteins and assessing IDPs structures. PMID:28097742

  11. Ultrafast dynamics of nonequilibrium resonance energy transfer and probing globular protein flexibility of myoglobin.

    PubMed

    Stevens, Jeffrey A; Link, Justin J; Zang, Chen; Wang, Lijuan; Zhong, Dongping

    2012-03-22

    Protein structural plasticity is critical to many biological activities and accurate determination of its temporal and spatial fluctuations is challenging and difficult. Here, we report our extensive characterization of global flexibility of a globular heme protein of myoglobin using resonance energy transfer as a molecular ruler. With site-directed mutagenesis, we use a tryptophan scan to examine local structural fluctuations from B to H helices utilizing 10 tryptophan-heme energy transfer pairs with femtosecond resolution. We observed ultrafast resonance energy transfer dynamics by following a nearly single exponential behavior in 10-100 ps, strongly indicating that the globular structure of myoglobin is relatively rigid, with no observable static or slow dynamic conformational heterogeneity. The observation is against our molecular dynamics simulations, which show large local fluctuations and give multiple exponential energy transfer behaviors, suggesting too flexible of the global structure and thus raising a serious issue of the force fields used in simulations. Finally, these ultrafast energy transfer dynamics all occur on the similar time scales of local environmental relaxations (solvation), leading to nonexponential processes caused by energy relaxations, not structural fluctuations. Our analyses of such processes reveal an intrinsic compressed- and/or stretched-exponential behaviors and elucidate the nature of inherent nonequilibrium of ultrafast resonance energy transfer in proteins. This new concept of compressed nonequilibrium transfer dynamics should be applied to all protein studies by time-resolved Förster resonance energy transfer (FRET).

  12. CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Statistical interior properties of globular proteins

    NASA Astrophysics Data System (ADS)

    Jiang, Zhou-Ting; Zhang, Lin-Xi; Sun, Ting-Ting; Wu, Tai-Quan

    2009-10-01

    The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters NC and ND are defined to confine the valid residues in detail. The relationship between hydrophobicity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage Pi and sequential residue length Li of a certain protein i are calculated under different conditions. The statistical results show that the average value of Pi as well as Li of all-α proteins has a minimum among these 4 classes of globular proteins, indicating that all-α proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-β proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of β sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.

  13. Nucleation and Crystallization of Globular Proteins: What we Know and What is Missing

    NASA Technical Reports Server (NTRS)

    Rosenberger, F.; Vekilov, P. G.; Muschol, M.; Thomas, B. R.

    1996-01-01

    Recently. much progress has been made in understanding the nucleation and crystallization of globular proteins, including the formation of compositional and structural crystal defects, Insight into the interactions of (screened) protein macro-ions in solution, obtained from light scattering, small angle X-ray scattering and osmotic pressure studies. can guide the search for crystallization conditions. These studies show that the nucleation of globular proteins is governed by the same principles as that of small molecules. However, failure to account for direct and indirect (hydrodynamic) protein interactions in the solutions results in unrealistic aggregation scenarios. Microscopic studies of numerous proteins reveal that crystals grow by the attachment of growth units through the same layer-spreading mechanisms as inorganic crystals. Investigations of the growth kinetics of hen-egg-white lysozyme (HEWL) reveal non-steady behavior under steady external conditions. Long-term variations in growth rates are due to changes in step-originating dislocation groups. Fluctuations on a shorter timescale reflect the non-linear dynamics of layer growth that results from the interplay between interfacial kinetics and bulk transport. Systematic gel electrophoretic analyses suggest that most HEWL crystallization studies have been performed with material containing other proteins at percent levels. Yet, sub-percent levels of protein impurities impede growth step propagation and play a role in the formation of structural/compositional inhomogeneities. In crystal growth from highly purified HEWL solutions, however, such inhomogeneities are much weaker and form only in response to unusually large changes in growth conditions. Equally important for connecting growth conditions to crystal perfection and diffraction resolution are recent advances in structural characterization through high-resolution Bragg reflection profiling and X-ray topography.

  14. Prediction of heat-induced polymerization of different globular food proteins in mixtures with wheat gluten.

    PubMed

    Lambrecht, Marlies A; Rombouts, Ine; De Ketelaere, Bart; Delcour, Jan A

    2017-04-15

    Egg, soy or whey protein co-exists with wheat gluten in different food products. Different protein types impact each other during heat treatment. A positive co-protein effect occurs when heat-induced polymerization of a mixture of proteins is more intense than that of the isolated proteins. The intrinsic protein characteristics of globular proteins which enhance polymerization in mixtures with gluten are unknown. In this report, a model was developed to predict potential co-protein effects in mixtures of gluten and globular proteins during heating at 100°C. A negative co-protein effect with addition of lysozyme, no co-protein effect with soy glycinin or egg yolk and positive co-protein effects with bovine serum albumin, (S-)ovalbumin, egg white, whole egg, defatted egg yolk, wheat albumins and wheat globulins were detected. The level of accessible free sulfhydryl groups and the surface hydrophobicity of unfolded globular proteins were the main characteristics in determining the co-protein effects in gluten mixtures.

  15. Canine Distemper Virus Envelope Protein Interactions Modulated by Hydrophobic Residues in the Fusion Protein Globular Head

    PubMed Central

    Avila, Mislay; Khosravi, Mojtaba; Alves, Lisa; Ader-Ebert, Nadine; Bringolf, Fanny; Zurbriggen, Andreas; Plemper, Richard K.

    2014-01-01

    Membrane fusion for morbillivirus cell entry relies on critical interactions between the viral fusion (F) and attachment (H) envelope glycoproteins. Through extensive mutagenesis of an F cavity recently proposed to contribute to F's interaction with the H protein, we identified two neighboring hydrophobic residues responsible for severe F-to-H binding and fusion-triggering deficiencies when they were mutated in combination. Since both residues reside on one side of the F cavity, the data suggest that H binds the F globular head domain sideways. PMID:25355896

  16. VARIABLE STARS IN LARGE MAGELLANIC CLOUD GLOBULAR CLUSTERS. II. NGC 1786

    SciTech Connect

    Kuehn, Charles A.; Smith, Horace A.; De Lee, Nathan; Catelan, Marcio; Pritzl, Barton J.; Borissova, Jura E-mail: smith@pa.msu.edu E-mail: mcatelan@astro.puc.cl E-mail: jura.borissova@uv.cl

    2012-12-01

    This is the second in a series of papers studying the variable stars in Large Magellanic Cloud globular clusters. The primary goal of this series is to study how RR Lyrae stars in Oosterhoff-intermediate systems compare to their counterparts in Oosterhoff I/II systems. In this paper, we present the results of our new time-series B-V photometric study of the globular cluster NGC 1786. A total of 65 variable stars were identified in our field of view. These variables include 53 RR Lyraes (27 RRab, 18 RRc, and 8 RRd), 3 classical Cepheids, 1 Type II Cepheid, 1 Anomalous Cepheid, 2 eclipsing binaries, 3 Delta Scuti/SX Phoenicis variables, and 2 variables of undetermined type. Photometric parameters for these variables are presented. We present physical properties for some of the RR Lyrae stars, derived from Fourier analysis of their light curves. We discuss several different indicators of Oosterhoff type which indicate that the Oosterhoff classification of NGC 1786 is not as clear cut as what is seen in most globular clusters.

  17. How round is a protein? Exploring protein structures for globularity using conformal mapping.

    PubMed

    Hass, Joel; Koehl, Patrice

    2014-01-01

    We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy E S (f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that E S (f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy E S (f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that E S (f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry.

  18. [Long-range electron transfer in globular proteins by polaron excitation].

    PubMed

    Lakhno, V L; Chuev, G N

    1997-01-01

    Considering polaron model, we have calculated an electron state localized in the protein heme. Using these calculations: the electron density and electron energy, we estimated the self-exchange rate constant for cyt c (horse heart), its reorganization energy, matrix element, and dependence of this rate on the distance between hemes. The results are compared with the experimental data and other theoretical estimations. We discuss the role of polaron excitations in the long-range electron transfer in globular proteins.

  19. High pressure effects on the structural functionality of condensed globular-protein matrices.

    PubMed

    Savadkoohi, Sobhan; Kasapis, Stefan

    2016-07-01

    High pressure technology is the outcome of consumer demand for better quality control of processed foods. There is great potential to apply HPP to condensed systems of globular proteins for the generation of industry-relevant biomaterials with advanced techno- and biofunctionality. To this end, research demonstrates that application of high hydrostatic pressure generates a coherent structure and preserves the native conformation in condensed globular proteins, which is an entirely unexpected but interesting outcome on both scientific and technological grounds. In microbiological challenge tests, high pressure at conventional commercial conditions, demonstrated to effectively reduce the concentration of typical Gram negative or Gram positive foodborne pathogens, and proteolytic enzymes in high-solid protein samples. This may have industrial significance in relation to the formulation and stabilisation of "functional food" products as well as in protein ingredients and concentrates by replacing spray dried powders with condensed HPP-treated pastes that maintain structure and bioactivity. Fundamental concepts and structural functionality of condensed matrices of globular proteins are the primary interest in this mini-review, which may lead to opportunities for industrial exploitation, but earlier work on low-solid systems is also summarised presently to put recent developments in context of this rapidly growing field.

  20. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation.

    PubMed Central

    Thomas, P. D.; Dill, K. A.

    1993-01-01

    How important are helical propensities in determining the conformations of globular proteins? Using the two-dimensional lattice model and two monomer types, H (hydrophobic) and P (polar), we explore both nonlocal interactions, through an HH contact energy, epsilon, as developed in earlier work, and local interactions, through a helix energy, sigma. By computer enumeration, the partition functions for short chains are obtained without approximation for the full range of both types of energy. When nonlocal interactions dominate, some sequences undergo coil-globule collapse to a unique native structure. When local interactions dominate, all sequences undergo helix-coil transitions. For two different conformational properties, the closest correspondence between the lattice model and proteins in the Protein Data Bank is obtained if the model local interactions are made small compared to the HH contact interaction, suggesting that helical propensities may be only weak determinants of globular protein structures in water. For some HP sequences, varying sigma/epsilon leads to additional sharp transitions (sometimes several) and to "conformational switching" between unique conformations. This behavior resembles the transitions of globular proteins in water to helical states in alcohols. In particular, comparison with experiments shows that whereas urea as a denaturant is best modeled as weakening both local and nonlocal interactions, trifluoro-ethanol is best modeled as mainly weakening HH interactions and slightly enhancing local helical interactions. PMID:8298455

  1. Variable Stars in Large Magellanic Cloud Globular Clusters. II. NGC 1786

    NASA Astrophysics Data System (ADS)

    Kuehn, Charles A.; Smith, Horace A.; Catelan, Márcio; Pritzl, Barton J.; De Lee, Nathan; Borissova, Jura

    2012-12-01

    This is the second in a series of papers studying the variable stars in Large Magellanic Cloud globular clusters. The primary goal of this series is to study how RR Lyrae stars in Oosterhoff-intermediate systems compare to their counterparts in Oosterhoff I/II systems. In this paper, we present the results of our new time-series B-V photometric study of the globular cluster NGC 1786. A total of 65 variable stars were identified in our field of view. These variables include 53 RR Lyraes (27 RRab, 18 RRc, and 8 RRd), 3 classical Cepheids, 1 Type II Cepheid, 1 Anomalous Cepheid, 2 eclipsing binaries, 3 Delta Scuti/SX Phoenicis variables, and 2 variables of undetermined type. Photometric parameters for these variables are presented. We present physical properties for some of the RR Lyrae stars, derived from Fourier analysis of their light curves. We discuss several different indicators of Oosterhoff type which indicate that the Oosterhoff classification of NGC 1786 is not as clear cut as what is seen in most globular clusters. Based on observations taken with the SMARTS 1.3 m telescope operated by the SMARTS Consortium and observations taken at the Southern Astrophysical Research (SOAR) telescope, which is a joint project of the Ministério da Ciência, Tecnologia, e Inovação (MCTI) da República Federativa do Brasil, the U.S. National Optical Astronomy Observatory (NOAO), the University of North Carolina at Chapel Hill (UNC), and Michigan State University (MSU).

  2. Structural hot spots for the solubility of globular proteins.

    PubMed

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-02-24

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function.

  3. Structural hot spots for the solubility of globular proteins

    PubMed Central

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-01-01

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

  4. Superexchange coupling and electron transfer in globular proteins via polaron excitations.

    PubMed

    Chuev, G N; Lakhno, V D; Ustitnin, M N

    1999-06-01

    The polaron approach is used to treat long-range electron transfers between globular proteins. A rate expression for the polaron transfer model is given along with a description of appropriate conditions for its use. Assuming that electrons transfer via a superexchange coupling due to a polaron excitation, we have estimated the distance dependence of the rate constant for the self-exchange reactions between globular proteins in solutions. The distance dependence of the polaron coupling and solvent reorganization energy are provided as a basis for understanding and interpreting a long-range electron transfer experiment. The difficulties and problems of the polaron treatment of long-range electron transfers are discussed, and suggestions for new experiments are made.

  5. Chemical Abundances of Two Stars in the Large Magellanic Cloud Globular Cluster NGC 1718

    NASA Astrophysics Data System (ADS)

    Sakari, Charli M.; McWilliam, Andrew; Wallerstein, George

    2017-01-01

    Detailed chemical abundances of two stars in the intermediate-age Large Magellanic Cloud (LMC) globular cluster NGC 1718 are presented, based on high resolution spectroscopic observations with the MIKE spectrograph. The detailed abundances confirm NGC 1718 to be a fairly metal-rich cluster, with an average [{Fe/H}] ˜ -0.55± 0.01. The two red giants appear to have primordial O, Na, Mg, and Al abundances, with no convincing signs of a composition difference between the two stars-hence, based on these two stars, NGC 1718 shows no evidence for hosting multiple populations. The Mg abundance is lower than Milky Way field stars, but is similar to LMC field stars at the same metallicity. The previous claims of very low [Mg/Fe] in NGC 1718 are therefore not supported in this study. Other abundances (Si, Ca, Ti, V, Mn, Ni, Cu, Rb, Y, Zr, La, and Eu) all follow the LMC field star trend, demonstrating yet again that (for most elements) globular clusters trace the abundances of their host galaxy's field stars. Similar to the field stars, NGC 1718 is found to be mildly deficient in explosive α-elements, but moderately to strongly deficient in O, Na, Mg, Al, and Cu, elements which form during hydrostatic burning in massive stars. NGC 1718 is also enhanced in La, suggesting that it was enriched in ejecta from metal-poor AGB stars.

  6. Three Classes of Motion in the Dynamic Neutron-Scattering Susceptibility of a Globular Protein

    SciTech Connect

    Hong, Liang; Lindner, Benjamin; Smolin, Nikolai; Sokolov, Alexei P; Smith, Jeremy C

    2011-01-01

    A simplified description of the 295 K dynamics of a globular protein over a wide frequency range (1 1000 GHz) is obtained by combining neutron scattering of lysozyme with molecular dynamics simulation. The molecular dynamics simulation agrees quantitatively with experiment for both the protein and the hydration water and shows that, whereas the hydration water molecules subdiffuse, the protein atoms undergo confined motion decomposable into three distinct classes: localized diffusion, methyl group rotations, and jumps. Each of the three classes gives rise to a characteristic neutron susceptibility signal.

  7. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins.

    PubMed

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.

  8. A FOSSIL BULGE GLOBULAR CLUSTER REVEALED BY VERY LARGE TELESCOPE MULTI-CONJUGATE ADAPTIVE OPTICS

    SciTech Connect

    Ortolani, Sergio; Barbuy, Beatriz; Momany, Yazan; Saviane, Ivo; Jilkova, Lucie; Bica, Eduardo; Salerno, Gustavo M.; Jungwiert, Bruno E-mail: barbuy@astro.iag.usp.br E-mail: isaviane@eso.org E-mail: bica@if.ufrgs.br

    2011-08-10

    The globular cluster HP 1 is projected on the bulge, very close to the Galactic center. The Multi-Conjugate Adaptive Optics Demonstrator on the Very Large Telescope allowed us to acquire high-resolution deep images that, combined with first epoch New Technology Telescope data, enabled us to derive accurate proper motions. The cluster and bulge fields' stellar contents were disentangled through this process and produced an unprecedented definition in color-magnitude diagrams of this cluster. The metallicity of [Fe/H] {approx} -1.0 from previous spectroscopic analysis is confirmed, which together with an extended blue horizontal branch imply an age older than the halo average. Orbit reconstruction results suggest that HP 1 is spatially confined within the bulge.

  9. Comparison of heat-induced aggregation of globular proteins.

    PubMed

    Delahaije, Roy J B M; Wierenga, Peter A; Giuseppin, Marco L F; Gruppen, Harry

    2015-06-03

    Typically, heat-induced aggregation of proteins is studied using a single protein under various conditions (e.g., temperature). Because different studies use different conditions and methods, a mechanistic relationship between molecular properties and the aggregation behavior of proteins has not been identified. Therefore, this study investigates the kinetics of heat-induced aggregation and the size/density of formed aggregates for three different proteins (ovalbumin, β-lactoglobulin, and patatin) under various conditions (pH, ionic strength, concentration, and temperature). The aggregation rate of β-lactoglobulin was slower (>10 times) than that of ovalbumin and patatin. Moreover, the conditions (pH, ionic strength, and concentration) affected the aggregation kinetics of β-lactoglobulin more strongly than for ovalbumin and patatin. In contrast to the kinetics, for all proteins the aggregate size/density increased with decreasing electrostatic repulsion. By comparing these proteins under these conditions, it became clear that the aggregation behavior cannot easily be correlated to the molecular properties (e.g., charge and exposed hydrophobicity).

  10. Dynamics of a globular protein and its hydration water studied by neutron scattering and MD simulations

    DOE PAGES

    Chen, Sow-Hsin; Lagi, Marco; Chu, Xiang-qiang; ...

    2010-01-01

    This review article describes our neutron scattering experiments made in the past four years for the understanding of the single-particle (hydrogen atom) dynamics of a protein and its hydration water and the strong coupling between them. We found that the key to this strong coupling is the existence of a fragile-to-strong dynamic crossover (FSC) phenomenon occurring at around T L = 225±5 K in the hydration water. On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the high density form (HDL), a more fluid state, to predominantly the low density formmore » (LDL), a less fluid state, derived from the existence of a liquid–liquid critical point at an elevated pressure. We show experimentally that this sudden switch in the mobility of hydration water on Lysozyme, B-DNA and RNA triggers the dynamic transition, at a temperature T D = 220 K, for these biopolymers. In the glassy state, below T D , the biopolymers lose their vital conformational flexibility resulting in a substantial diminishing of their biological functions. We also performed molecular dynamics (MD) simulations on a realistic model of hydrated lysozyme powder, which confirms the existence of the FSC and the hydration level dependence of the FSC temperature. Furthermore, we show a striking feature in the short time relaxation ( β -relaxation) of protein dynamics, which is the logarithmic decay spanning 3 decades (from ps to ns). The long time α -relaxation shows instead a diffusive behavior, which supports the liquid-like motions of protein constituents. We then discuss our recent high-resolution X-ray inelastic scattering studies of globular proteins, Lysozyme and Bovine Serum Albumin. We were able to measure the dispersion relations of collective, intra-protein phonon-like excitations in these proteins for the first time. We found that the phonon energies show a marked softening and at the same time their population increases

  11. Interaction of Globular Plasma Proteins with Water-Soluble CdSe Quantum Dots.

    PubMed

    Pathak, Jyotsana; Rawat, Kamla; Sanwlani, Shilpa; Bohidar, H B

    2015-06-08

    The interactions between water-soluble semiconductor quantum dots [hydrophilic 3-mercaptopropionic acid (MPA)-coated CdSe] and three globular plasma proteins, namely, bovine serum albumin (BSA), β-lactoglobulin (β-Lg) and human serum albumin (HSA), are investigated. Acidic residues of protein molecules form electrostatic interactions with these quantum dots (QDs). To determine the stoichiometry of proteins bound to QDs, we used dynamic light scattering (DLS) and zeta potential techniques. Fluorescence resonance energy transfer (FRET) experiments revealed energy transfer from tryptophan residues in the proteins to the QD particles. Quenching of the intrinsic fluorescence of protein molecules was noticed during this binding process (hierarchy HSA<β-Lg protein molecules). Upon binding with QD particles, the protein molecules underwent substantial conformational changes at the secondary-structure level (50 % helicity lost), due to loss in hydration.

  12. A polaron model for electron transfer in globular proteins.

    PubMed

    Chuev, G N; Lakhno, V D

    1993-07-07

    Polaron models have been considered for the electron states in protein globules existing in a solvent. These models account for two fundamental effects, viz, polarization interaction of an electron with the conformational vibrations and the heterogeneity of the medium. Equations have been derived to determine the electron state in a protein globule. The parameters of this state show that it is an extended state with an energy of 2 eV. The electron transfer rate for cyt C self-exchange reaction has been calculated in the polaron model. Reorganization energy, tunneling matrix element and the rate constant have also been estimated. The results are compared with experimental data. The influence of model parameters on the significance of the data obtained has been studied. The potentialities of the model are discussed.

  13. Prediction of functionally important residues in globular proteins from unusual central distances of amino acids

    PubMed Central

    2011-01-01

    Background Well-performing automated protein function recognition approaches usually comprise several complementary techniques. Beside constructing better consensus, their predictive power can be improved by either adding or refining independent modules that explore orthogonal features of proteins. In this work, we demonstrated how the exploration of global atomic distributions can be used to indicate functionally important residues. Results Using a set of carefully selected globular proteins, we parametrized continuous probability density functions describing preferred central distances of individual protein atoms. Relative preferred burials were estimated using mixture models of radial density functions dependent on the amino acid composition of a protein under consideration. The unexpectedness of extraordinary locations of atoms was evaluated in the information-theoretic manner and used directly for the identification of key amino acids. In the validation study, we tested capabilities of a tool built upon our approach, called SurpResi, by searching for binding sites interacting with ligands. The tool indicated multiple candidate sites achieving success rates comparable to several geometric methods. We also showed that the unexpectedness is a property of regions involved in protein-protein interactions, and thus can be used for the ranking of protein docking predictions. The computational approach implemented in this work is freely available via a Web interface at http://www.bioinformatics.org/surpresi. Conclusions Probabilistic analysis of atomic central distances in globular proteins is capable of capturing distinct orientational preferences of amino acids as resulting from different sizes, charges and hydrophobic characters of their side chains. When idealized spatial preferences can be inferred from the sole amino acid composition of a protein, residues located in hydrophobically unfavorable environments can be easily detected. Such residues turn out to be

  14. Equilibrium properties of realistic random heteropolymers and their relevance for globular and naturally unfolded proteins

    NASA Astrophysics Data System (ADS)

    Tiana, G.; Sutto, L.

    2011-12-01

    Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been studied with mean-field models in the thermodynamic limit, or with computer simulations of very small chains on lattice. After describing a self-adjusting parallel-tempering technique to sample efficiently the low-energy states of frustrated systems without the need of tuning the system-dependent parameters of the algorithm, we apply it to random heteropolymers moving in continuous space. We show that if the mean interaction between monomers is negative, the usual description through the random-energy model is nearly correct, provided that it is extended to account for noncompact conformations. If the mean interaction is positive, such a simple description breaks out and the system behaves in a way more similar to Ising spin glasses. The former case is a model for the denatured state of globular proteins, the latter of naturally unfolded proteins, whose equilibrium properties thus result as qualitatively different.

  15. Superexchange coupling and electron transfer in globular proteins via polaron excitations.

    PubMed

    Chuev, G N; Lakhno, V D; Ustitnin, M N

    2000-06-01

    The polaron approach is used to treat long-range electron transfersbetween globular proteins. A rate expression for the polaron transfer model is given along with a description of appropriate conditions forits use. Assuming that electrons transfer via a superexchange couplingdue to a polaron excitation, we have estimated the distance dependenceof the rate constant for the self-exchange reactions between globularproteins in solutions. The distance dependence of the polaron coupling andsolvent reorganization energy are provided as a basis forunderstanding and interpreting a long-range electron transfer experiment.The difficulties and problems of the polaron treatment of long-rangeelectron transfers are discussed, and suggestions for new experimentsare made.

  16. SANS study of understanding mechanism of cold gelation of globular proteins

    SciTech Connect

    Chinchalikar, A. J. Kumar, Sugam Aswal, V. K. Wagh, A. G.; Kohlbrecher, J.

    2014-04-24

    Small-angle neutron scattering (SANS) has been used to probe the evolution of interaction and the resultant structures in the cold gelation of globular proteins. The cold gelation involves two steps consisting of irreversible protein deformation by heating followed by some means (e.g. increasing ionic strength) to bring them together at room temperature. We have examined the role of different salts in cold gelation of preheated aqueous Bovine Serum Albumin (BSA) protein solutions. The interactions have been modeled by two Yukawa potential combining short-range attraction and long-range repulsion. We show that in step 1 (preheated temperature effect) the deformation of protein increases the magnitude of attractive interaction but not sufficient to induce gel. The attractive interaction is further enhanced in step 2 (salt effect) to result in gel formation. The salt effect is found to be strongly depending on the valency of the counterions. The gel structure has been characterized by the mass fractals.

  17. The recombinant globular head domain of the measles virus hemagglutinin protein as a subunit vaccine against measles.

    PubMed

    Lobanova, Liubov M; Eng, Nelson F; Satkunarajah, Malathy; Mutwiri, George K; Rini, James M; Zakhartchouk, Alexander N

    2012-04-26

    Despite the availability of live attenuated measles virus (MV) vaccines, a large number of measles-associated deaths occur among infants in developing countries. The development of a measles subunit vaccine may circumvent the limitations associated with the current live attenuated vaccines and eventually contribute to global measles eradication. Therefore, the goal of this study was to test the feasibility of producing the recombinant globular head domain of the MV hemagglutinin (H) protein by stably transfected human cells and to examine the ability of this recombinant protein to elicit MV-specific immune responses. The recombinant protein was purified from the culture supernatant of stably transfected HEK293T cells secreting a tagged version of the protein. Two subcutaneous immunizations with the purified recombinant protein alone resulted in the production of MV-specific serum IgG and neutralizing antibodies in mice. Formulation of the protein with adjuvants (polyphosphazene or alum) further enhanced the humoral immune response and in addition resulted in the induction of cell-mediated immunity as measured by the production of MV H-specific interferon gamma (IFN-γ) and interleukin 5 (IL-5) by in vitro re-stimulated splenocytes. Furthermore, the inclusion of polyphosphazene into the vaccine formulation induced a mixed Th1/Th2-type immune response. In addition, the purified recombinant protein retained its immunogenicity even after storage at 37°C for 2 weeks.

  18. The merger remnant NGC 3610 and its globular cluster system: a large-scale study

    NASA Astrophysics Data System (ADS)

    Bassino, Lilia P.; Caso, Juan P.

    2017-01-01

    We present a photometric study of the prototype merger remnant NGC 3610 and its globular cluster (GC) system, based on new GEMINI/GMOS and ACS/HST archival images. Thanks to the large FOV of our GMOS data, larger than previous studies, we are able to detect a `classical' bimodal GC colour distribution, correponding metal-poor and metal-rich GCs, at intermediate radii and a small subsample of likely young clusters of intermediate colours, mainly located in the outskirts. The extent of the whole GC system is settled as about 40 kpc. The GC population is quite poor, about 500 ± 110 members that corresponds to a low total specific frequency SN ˜ 0.8. The effective radii of a cluster sample are determined, including those of two spectroscopically confirmed young and metal-rich clusters, that are in the limit between GC and UCD sizes and brightness. The large-scale galaxy surface-brightness profile can be decomposed as an inner embedded disc and an outer spheroid, determining for both larger extents than earlier research (10 kpc and 30 kpc, respectively). We detect boxy isophotes, expected in merger remnants, and show a wealth of fine-structure in the surface-brightness distribution with unprecedented detail, coincident with the outer spheroid. The lack of symmetry in the galaxy colour map adds a new piece of evidence to the recent merger scenario of NGC 3610.

  19. A Large Sample Sodium and Magnesium Abundance Study in the Globular Cluster M3 (NGC 5272)

    NASA Astrophysics Data System (ADS)

    Johnson, C. I.; Sneden, C.; Pilachowski, C. A.; Guntel, B.; Kraft, R. P.; Ivans, I. I.

    2005-09-01

    We have derived sodium and magnesium abundances for more than 100 red giant branch (RGB) stars in the Galactic globular cluster M3 (NGC 5272), using moderate resolving power (R˜20,000) spectra obtained with the WIYN telescope and Hydra multi-fiber spectrograph. Temperatures for the M3 sample are based on calibrations of photometric indices, in particular V-K. Gravities, microturbulent velocities, and the overall M3 metallicity ([Fe/H]˜--1.5) are based on earlier high-resolution spectroscopic analyses. Na and Mg abundances have been determined from observed/synthetic spectrum matches of the 5682, 5688 Å Na I lines and the 5711 Å Mg I line. The resulting M3 abundances are compared with the more detailed analyses of a smaller sample of M3 RGB stars observed at very high spectral resolution with the Keck I HIRES instrument, and with a similarly large-sample data set previously obtained for M13. We conclude that the star-to-star variation in sodium is greater than that of magnesium in both clusters and also that M13 contains a higher population of low sodium, high magnesium stars than does M3.

  20. VARIABLE STARS IN LARGE MAGELLANIC CLOUD GLOBULAR CLUSTERS. I. NGC 1466

    SciTech Connect

    Kuehn, Charles A.; Smith, Horace A.; De Lee, Nathan; Catelan, Marcio; Pritzl, Barton J.; Borissova, Jura E-mail: smith@pa.msu.edu E-mail: mcatelan@astro.puc.cl E-mail: jura.borissova@uv.cl

    2011-10-15

    This is the first in a series of papers studying the variable stars in Large Magellanic Cloud globular clusters. The primary goal of this series is to better understand how the RR Lyrae stars in Oosterhoff-intermediate systems compare to those in Oosterhoff I/II systems. In this paper, we present the results of our new time-series BV photometric study of NGC 1466. A total of 62 variables were identified in the cluster, of which 16 are new discoveries. The variables include 30 RRab stars, 11 RRc stars, 8 RRd stars, 1 candidate RR Lyrae, 2 long-period variables, 1 potential anomalous Cepheid, and 9 variables of undetermined classification. We present photometric parameters for these variables. For the RR Lyrae stars physical properties derived from Fourier analysis of their light curves are presented. The RR Lyrae stars were used to determine a reddening-corrected distance modulus of (m - M){sub 0} = 18.43 {+-} 0.15. We discuss several different indicators of Oosterhoff type and find NGC 1466 to be an Oosterhoff-intermediate object.

  1. [Electron transfer between globular proteins. Dependence of the rate of transfer on distance].

    PubMed

    Lakhno, V D; Chuev, G N; Ustinin, M N; Komarov, V M

    1998-01-01

    Based on the assumption that electron transfer between globular proteins occurs by a collective excitation of polaron type, the dependence of the rate of this process on the distance between the donor and acceptor centers with regard to their detailed electron structure was calculated. The electron structure of the heme was calculated by the quantum-chemical MNDO-PM3 method. The results were compared with experimental data on interprotein and intraglobular electron transfer. It is shown that, in the framework of this model, the electron transfer is not exponential and does not require a particular transfer pathway since the whole protein macromolecule is involved in the formation of the electron excited state.

  2. Thermodynamics of the interaction of globular proteins with powdered stearic acid in acid pH.

    PubMed

    Mitra, Atanu; Chattoraj, D K; Chakraborty, P

    2006-06-01

    Adsorption isotherms of different globular proteins and gelatin on strearic acid particles have been studied as a function of biopolymer concentration, ionic strength of the medium, and temperature. The effect of neutral salts including CaCl2, Na3PO4, and urea on the adsorption isotherms has been also investigated. It is observed that the extent of adsorption (Gamma2(1)) increases in two steps with the increase of biopolymer concentration (C2) in the bulk. Gamma2(1) increases with an increase of C2 until a steady maximum value Gamma2(m) is reached at a critical concentration C2(m). After initial saturation, Gamma2(1) again increases from Gamma2(m) without reaching any limiting value due to the surface aggregation of the protein. The values of the standard free energy change for adsorption have been calculated on the basis of the Gibbs equation. The standard entropy and enthalpy changes are also calculated.

  3. Fluorescence based assessment of SDS induced hydrophobic collapse in globular proteins

    NASA Astrophysics Data System (ADS)

    Manjunath, S.; Makani, Venkata Krishna Kanth; Satyamoorthy, Kapaettu; Rao, Bola Sadashiva Satish; Bhat, Gopalkrishna; Kanth, Akriti Baby; Mahato, Krishna Kishore

    2016-03-01

    The molecular mechanism of interaction between SDS and proteins is not clearly understood so far. According to the current knowledge SDS is known to interact with the hydrophobic regions of the proteins. Tryptophan and tyrosine are hydrophobic and hydrophilic aromatic amino acids respectively, which are also known for their intrinsic fluorescence nature in proteins. By observing the autofluorescence of both these hydrophobic and hydrophilic amino acids upon SDS treatment, information about SDS-protein interactions could be obtained. In the present study we have recorded the autofluorescence spectra of five globular proteins [Bovine serum albumin (BSA), Human serum albumin (HSA), Ribonuclease A (RNase A), Lysozyme and Trypsin] by the sequential excitation from 260nm to 295nm at every 5nm intervals. The results obtained clearly indicated BSA and HSA undergone hydrophobic collapse around their tryptophan moieties due to the increased folding of their secondary and tertiary structures upon SDS treatment. Trypsin on the other hand showed complete unfolding upon treatment with SDS. Lysozyme and RNase A did not show any difference in their autofluorescence upon SDS treatment may be due to the stability and fluorophores composition in them. The above results obtained with specific UV excitations clearly shown the tertiary folding and ensembles of the secondary and tertiary structures upon SDS treatment is governed by their stability and bonds stabilizing the proteins.

  4. Unusual Dynamics of Concentration Fluctuations in Solutions of Weakly Attractive Globular Proteins

    PubMed Central

    2015-01-01

    The globular protein γB-crystallin exhibits a complex phase behavior, where liquid–liquid phase separation characterized by a critical volume fraction ϕc = 0.154 and a critical temperature Tc = 291.8 K coexists with dynamical arrest on all length scales at volume fractions around ϕ ≈ 0.3–0.35, and an arrest line that extends well into the unstable region below the spinodal. However, although the static properties such as the osmotic compressibility and the static correlation length are in quantitative agreement with predictions for binary liquid mixtures, this is not the case for the dynamics of concentration fluctuations described by the dynamic structure factor S(q,t). Using a combination of dynamic light scattering and neutron spin echo measurements, we demonstrate that the competition between critical slowing down and dynamical arrest results in a much more complex wave vector dependence of S(q,t) than previously anticipated. PMID:26505877

  5. Beyond the brim of the hat: Kinematics of globular clusters out to large radii in the Sombrero galaxy

    SciTech Connect

    Dowell, Jessica L.; Rhode, Katherine L.; Bridges, Terry J.; Zepf, Stephen E.; Gebhardt, Karl; Freeman, Ken C.; De Boer, Elizabeth Wylie E-mail: rhode@astro.indiana.edu E-mail: zepf@pa.msu.edu E-mail: kcf@mso.anu.edu.au

    2014-06-01

    We have obtained radial velocity measurements for 51 new globular clusters around the Sombrero galaxy. These measurements were obtained using spectroscopic observations from the AAOmega spectrograph on the Anglo-Australian Telescope and the Hydra spectrograph at WIYN. Combining our own past measurements and velocity measurements obtained from the literature, we have constructed a large database of radial velocities that contains a total of 360 confirmed globular clusters. Previous studies' analyses of the kinematics and mass profile of the Sombrero globular cluster system have been constrained to the inner ∼9' (∼24 kpc or ∼5R{sub e} ), but our new measurements have increased the radial coverage of the data, allowing us to determine the kinematic properties of M104 out to ∼15' (∼41 kpc or ∼9R{sub e} ). We use our set of radial velocities to study the GC system kinematics and to determine the mass profile and V-band mass-to-light profile of the galaxy. We find that M/L{sub V} increases from 4.5 at the center to a value of 20.9 at 41 kpc (∼9R{sub e} or 15'), which implies that the dark matter halo extends to the edge of our available data set. We compare our mass profile at 20 kpc (∼4R{sub e} or ∼7.'4) to the mass computed from X-ray data and find good agreement. We also use our data to look for rotation in the globular cluster system as a whole, as well as in the red and blue subpopulations. We find no evidence for significant rotation in any of these samples.

  6. Integrated K-band spectra of old and intermediate-age globular clusters in the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Lyubenova, M.; Kuntschner, H.; Rejkuba, M.; Silva, D. R.; Kissler-Patig, M.; Tacconi-Garman, L. E.; Larsen, S. S.

    2010-02-01

    Current stellar population models have arguably the largest uncertainties in the near-IR wavelength range, partly due to a lack of large and well calibrated empirical spectral libraries. In this paper we present a project whose aim it is to provide the first library of luminosity weighted integrated near-IR spectra of globular clusters to be used to test the current stellar population models and serve as calibrators for future ones. Our pilot study presents spatially integrated K-band spectra of three old (≥10 Gyr) and metal poor ([Fe/H] ~ -1.4), and three intermediate age (1-2 Gyr) and more metal rich ([Fe/H] ~ - 0.4) globular clusters in the LMC. We measured the line strengths of the Na I, Ca I and 12CO (2-0) absorption features. The Na I index decreases with increasing age and decreasing metallicity of the clusters. The DCO index, used to measure the 12CO (2-0) line strength, is significantly reduced by the presence of carbon-rich TP-AGB stars in the globular clusters with age ~1 Gyr. This is in contradiction to the predictions of the stellar population models of Maraston (2005, MNRAS, 362, 799). We find that this disagreement is due to the different CO absorption strength of carbon-rich Milky Way TP-AGB stars used in the models and the LMC carbon stars in our sample. For globular clusters with age ≥ 2 Gyr we find DCO index measurements consistent with the model predictions. Based on observation collected at the ESO Paranal La Silla Observatory, Chile, Prog. ID 078.B-0205.Spectra in FITS format are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/510/A19

  7. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure.

    PubMed Central

    García De La Torre, J; Huertas, M L; Carrasco, B

    2000-01-01

    The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program. PMID:10653785

  8. Evidence for protein self-association induced by excluded volume. Myoglobin in the presence of globular proteins.

    PubMed

    Wilf, J; Minton, A P

    1981-10-28

    The fluorescence polarization of fluorescent derivatives of hemoglobin and myoglobin was measured as a function of the concentration of added polymers (PEG-6 000, PEG-20 000) and globular proteins (lysozyme, ribonuclease A, beta-lactoglobulin). The results indicated that the effective size and shape of 1-anilino-9-naphthalene sulfonate myoglobin are unaltered in the presence of up to 25 g/dl poly(ethylene glycol), whereas they are significantly altered in the presence of comparable concentrations of other proteins. The results are consistent with the hypothesis that in the presence of high concentrations of added protein, 1-anilino-9-naphthalene sulfonate myoglobin self-associates to form a dimer similar in size and shape to 1-anilino-9-naphthalene sulfonate hemoglobin.

  9. Effect of Small Molecule Osmolytes on the Self-Assembly and Functionality of Globular Protein-Polymer Diblock Copolymers

    SciTech Connect

    Thomas, Carla S.; Xu, Liza; Olsen, Bradley D.

    2013-12-05

    Blending the small molecule osmolytes glycerol and trehalose with the model globular protein–polymer block copolymer mCherry-b-poly(N-isopropyl acrylamide) (mCherry-b-PNIPAM) is demonstrated to improve protein functionality in self-assembled nanostructures. The incorporation of either additive into block copolymers results in functionality retention in the solid state of 80 and 100% for PNIPAM volume fractions of 40 and 55%, respectively. This represents a large improvement over the 50–60% functionality observed in the absence of any additive. Furthermore, glycerol decreases the thermal stability of block copolymer films by 15–20 °C, while trehalose results in an improvement in the thermal stability by 15–20 °C. These results suggest that hydrogen bond replacement is responsible for the retention of protein function but suppression or enhancement of thermal motion based on the glass transition of the osmolyte primarily determines thermal stability. While both osmolytes are observed to have a disordering effect on the nanostructure morphology with increasing concentration, this effect is less pronounced in materials with a larger polymer volume fraction. Glycerol preferentially localizes in the protein domains and swells the nanostructures, inducing disordering or a change in morphology depending on the PNIPAM coil fraction. In contrast, trehalose is observed to macrophase separate from the block copolymer, which results in nanodomains becoming more disordered without changing significantly in size.

  10. Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts

    NASA Astrophysics Data System (ADS)

    Yilmaz, Lutfu Safak; Atilgan, Ali Rana

    2000-09-01

    A low-resolution structural model based on the packing geometry of α-carbons is utilized to establish a connection between the flexible and rigid parts of a folded protein. The former commonly recognizes a complementing molecule for making a complex, while the latter manipulates the necessary conformational change for binding. We attempt analytically to distinguish this control architecture that intrinsically exists in globular proteins. First with two-dimensional simple models, then for a native protein, bovine pancreatic trypsin inhibitor, we explicitly demonstrate that inserting fluctuations in tertiary contacts supported by the stable core, one can regulate the displacement of residues on loop regions. The positional fluctuations of the flexible regions are annihilated by the rest of the protein in conformity with the Le Chatelier-Braun principle. The results indicate that the distortion of the principal nonbonded contacts between highly packed residues is accompanied by that of the slavery fluctuations that are widely distributed over the native structure. These positional arrangements do not appear in a reciprocal relation between a perturbation and the associated response; the effect of a movement of residue i on residue j is not equal to that of the same movement of residue j on residue i.

  11. Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins.

    PubMed

    García de la Torre, J

    2001-11-28

    The effect of hydration on hydrodynamic properties of globular proteins can be expressed in terms of two quantities: the delta (g/g) parameter and the thickness of the hydration layer. The two paradigms on hydration that originate these alternative measures are described and compared. For the numerical calculation of hydrodynamic properties, from which estimates of hydration can be made, we employ the bead modelling with atomic resolution implemented in programs HYDROPRO and HYDRONMR. As typical, average values, we find 0.3 g/g and a thickness of only approximately 1.2 A. However, noticeable differences in this parameter are found from one protein to another. We have made a numerical analysis, which leaves apart marginal influences of modelling imperfections by simulating properties of a spherical protein. This analysis confirms that the errors that one can attribute to the experimental quantities suffice to explain the observed fluctuations in the hydration parameters. However, for the main purpose of predicting protein solution properties, the above mentioned typical values may be safely used. Particularly for atomic bead modelling, a hydrodynamic radius of approximately 3.2 A yields predictions in very good agreement with experiments.

  12. Globular protein-coated Paclitaxel nanosuspensions: interaction mechanism, direct cytosolic delivery, and significant improvement in pharmacokinetics.

    PubMed

    Li, Yongji; Wu, Zhannan; He, Wei; Qin, Chao; Yao, Jing; Zhou, Jianping; Yin, Lifang

    2015-05-04

    About 40% of the marketed drugs and 70-90% of new drug candidates are insoluble in water and therefore poorly bioavailable, which significantly compromises their therapeutic effects. A formulation of nanosuspensions achieved by reducing the pure drug particle size down to seb-micron range is one of the most promising approaches to overcome the insolubility. However, the nanosuspension formulations are subject to instability because of nucleation and particle growth. Therefore, a stabilizer is needed to be incorporated into the nanosuspension formulation during the preparation process to suppress the aggregation of drug particles. β-LG, a globular protein, is broken by heat-induced denaturation, and its hydrophobic area is exposed, which allows it to associate with organic particles. PTX, an insoluble drug, is widely used for the clinical treatment of human cancer. However, this drug's clinical application is greatly limited by intrinsic defects including poor solubility, adverse side effects, and poor tumor penetration. In this study, we prepared β-LG-stabilized PTX nanosuspensions (PTX-NS) by coating the protein onto nanoscaled drug particles, investigating the stabilization effect of β-LG on PTX-NS, and evaluating its in vitro and in vivo performance. PTX-NS with a diameter of approximately 200 nm was easily prepared. β-LG produced significantly stabilized effect on PTX-NS via the interaction between the hydrophobic area of the protein and the hydrophobic surface of the drug particles, which resulted in a conformational change of the protein, the loss of both secondary and tertiary structures, and the transition of Trp residues to a less hydrophobic condition. Importantly, unlike other conventional nanoparticles, PTX-NS could directly translocated across the membrane into the cytosol in an energy-independent manner, without entrapment within the endosomal-lysosomal system. Moreover, compared with Taxol, PTX-NS increased AUC and Cmax by 26- and 16-fold

  13. Computational design of cyclic peptides for the customized oriented immobilization of globular proteins.

    PubMed

    Soler, Miguel A; Rodriguez, Alex; Russo, Anna; Adedeji, Abimbola Feyisara; Dongmo Foumthuim, Cedrix J; Cantarutti, Cristina; Ambrosetti, Elena; Casalis, Loredana; Corazza, Alessandra; Scoles, Giacinto; Marasco, Daniela; Laio, Alessandro; Fortuna, Sara

    2017-01-25

    The oriented immobilization of proteins, key for the development of novel responsive biomaterials, relies on the availability of effective probes. These are generally provided by standard approaches based on in vivo maturation and in vitro selection of antibodies and/or aptamers. These techniques can suffer technical problems when a non-immunogenic epitope needs to be targeted. Here we propose a strategy to circumvent this issue by in silico design. In our method molecular binders, in the form of cyclic peptides, are computationally evolved by stochastically exploring their sequence and structure space to identify high-affinity peptides for a chosen epitope of a target globular protein: here a solvent-exposed site of β2-microglobulin (β2m). Designed sequences were screened by explicit solvent molecular dynamics simulations (MD) followed by experimental validation. Five candidates gave dose-response surface plasmon resonance signals with dissociation constants in the micromolar range. One of them was further analyzed by means of isothermal titration calorimetry, nuclear magnetic resonance, and 250 ns of MD. Atomic-force microscopy imaging showed that this peptide is able to immobilize β2m on a gold surface. In short, we have shown by a variety of experimental techniques that it is possible to capture a protein through an epitope of choice by computational design.

  14. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

    PubMed Central

    Schwartz, Russell; Istrail, Sorin; King, Jonathan

    2001-01-01

    Patterns of hydrophobic and hydrophilic residues play a major role in protein folding and function. Long, predominantly hydrophobic strings of 20–22 amino acids each are associated with transmembrane helices and have been used to identify such sequences. Much less attention has been paid to hydrophobic sequences within globular proteins. In prior work on computer simulations of the competition between on-pathway folding and off-pathway aggregate formation, we found that long sequences of consecutive hydrophobic residues promoted aggregation within the model, even controlling for overall hydrophobic content. We report here on an analysis of the frequencies of different lengths of contiguous blocks of hydrophobic residues in a database of amino acid sequences of proteins of known structure. Sequences of three or more consecutive hydrophobic residues are found to be significantly less common in actual globular proteins than would be predicted if residues were selected independently. The result may reflect selection against long blocks of hydrophobic residues within globular proteins relative to what would be expected if residue hydrophobicities were independent of those of nearby residues in the sequence. PMID:11316883

  15. Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid

    PubMed Central

    Chan, Xin Yue

    2016-01-01

    Background Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. Methods In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratory Mtb. Results Genome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratory Mtb genomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated with Streptococcus pneumoniae meningitis and Neisseria meningitidis virulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study. Discussion The occurrence of in silico genetic differences in CSF-derived but not respiratory Mtb suggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal

  16. THE SURFACE-MEDIATED UNFOLDING KINETICS OF GLOBULAR PROTEINS IS DEPENDENT ON MOLECULAR WEIGHT AND TEMPERATURE

    SciTech Connect

    Patananan, A.N.; Goheen, S.C.

    2008-01-01

    The adsorption and unfolding pathways of proteins on rigid surfaces are essential in numerous complex processes associated with biomedical engineering, nanotechnology, and chromatography. It is now well accepted that the kinetics of unfolding are characterized by chemical and physical interactions dependent on protein deformability and structure, as well as environmental pH, temperature, and surface chemistry. Although this fundamental process has broad implications in medicine and industry, little is known about the mechanism because of the atomic lengths and rapid time scales involved. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the globular proteins to non-porous cationic polymer beads. The protein fractions were adsorbed at different residence times (0, 9, 10, 20, and 30 min) at near-physiological conditions using a gradient elution system similar to that in high-performance liquid chromatography. The elution profi les and retention times were obtained by ultraviolet/visible spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to irreversible protein unfolding on the non-porous surfaces. These data, and those of previous studies, fi t a positively increasing linear trend between percent unfolding after a fi xed (9 min) residence time (71.8%, 31.1%, and 32.1% of myoglobin, β-glucosidase, and ovalbumin, respectively) and molecular weight. Of all the proteins examined so far, only myoglobin deviated from this trend with higher than predicted unfolding rates. Myoglobin also exhibited an increase in retention time over a wide temperature range (0°C and 55°C, 4.39 min and 5.74 min, respectively) whereas ovalbumin and β-glucosidase did not. Further studies using a larger set of proteins are required to better understand the physiological and physiochemical implications of protein unfolding kinetics. This study confi rms that surface

  17. Disorder in Milk Proteins: α-Lactalbumin. Part B. A Multifunctional Whey Protein Acting as an Oligomeric Molten Globular "Oil Container" in the Anti-Tumorigenic Drugs, Liprotides.

    PubMed

    Uversky, Vladimir N; Permyakov, Serge E; Breydo, Leonid; Redwan, Elrashdy M; Almehdar, Hussein A; Permyakov, Eugene A

    2016-07-15

    This is a second part of the three-part article from a series of reviews on the abundance and roles of intrinsic disorder in milk proteins. We continue to describe α-lactalbumin, a small globular Ca2+-binding protein, which besides being one of the two components of lactose synthase that catalyzes the final step of the lactose biosynthesis in the lactating mammary gland, possesses a multitude of other functions. In fact, recent studies indicated that some partially folded forms of this protein possess noticeable bactericidal activity and other forms might be related to induction of the apoptosis of tumor cells. In its anti-tumorigenic function, oligomeric α-lactalbumin serves as a founding member of a new family of anticancer drugs termed liprotides (for lipids and partially denatured proteins), where an oligomeric molten globular protein acts as an "oil container" or cargo for the delivery of oleic acid to the cell membranes.

  18. Toward the description of electrostatic interactions between globular proteins: Potential of mean force in the primitive model

    NASA Astrophysics Data System (ADS)

    Dahirel, Vincent; Jardat, Marie; Dufrêche, Jean-François; Turq, Pierre

    2007-09-01

    Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern. Contrarily to Poisson-Boltzmann predictions, attractive, and repulsive direct forces between proteins are not screened similarly. Moreover, it has been shown that the relative orientations of the charge patterns strongly influence salt-mediated interactions. More precisely, for short distances between the proteins, ions enhance the difference of the effective forces between (i) like-charged and oppositely charged proteins, (ii) attractive and repulsive relative orientations of the proteins, which may affect the selectivity of protein/protein recognition. Finally, such results observed with the simplest models are applied to a more elaborate one to demonstrate their generality.

  19. Vibrational entropy of a protein: large differences between distinct conformations.

    PubMed

    Goethe, Martin; Fita, Ignacio; Rubi, J Miguel

    2015-01-13

    In this article, it is investigated whether vibrational entropy (VE) is an important contribution to the free energy of globular proteins at ambient conditions. VE represents the major configurational-entropy contribution of these proteins. By definition, it is an average of the configurational entropies of the protein within single minima of the energy landscape, weighted by their occupation probabilities. Its large part originates from thermal motion of flexible torsion angles giving rise to the finite peak widths observed in torsion angle distributions. While VE may affect the equilibrium properties of proteins, it is usually neglected in numerical calculations as its consideration is difficult. Moreover, it is sometimes believed that all well-packed conformations of a globular protein have similar VE anyway. Here, we measure explicitly the VE for six different conformations from simulation data of a test protein. Estimates are obtained using the quasi-harmonic approximation for three coordinate sets, Cartesian, bond-angle-torsion (BAT), and a new set termed rotamer-degeneracy lifted BAT coordinates by us. The new set gives improved estimates as it overcomes a known shortcoming of the quasi-harmonic approximation caused by multiply populated rotamer states, and it may serve for VE estimation of macromolecules in a very general context. The obtained VE values depend considerably on the type of coordinates used. However, for all coordinate sets we find large entropy differences between the conformations, of the order of the overall stability of the protein. This result may have important implications on the choice of free energy expressions used in software for protein structure prediction, protein design, and NMR refinement.

  20. The x ray population in globular clusters and three crab-like SNR in the large Magellanic cloud

    NASA Technical Reports Server (NTRS)

    Helfand, David J.

    1993-01-01

    This document is to serve as the requisite Final Technical Report on grant NAG5-1557 which was awarded under the NASA ROSAT Guest Investigator Program to Columbia University. In response to the NASA Research Anouncement describing the first round of Guest Investigations to be carried out under the U.S.-German ROSAT Program (AO-1), the PI submitted several proposals, three of which were accepted in part: (1) the x-ray population of globular clusters; (2) three crab-like SNR in the Large Magellanic Cloud; and (3) x rays from nearby radio pulsars. The status of these three programs as of 31 May 1993, the termination date of the grant, is reported.

  1. Prediction of exposure degree diagram and sites of limited proteolysis in globular proteins as an approach to computer-aided design of protein bioregulators with prolonged action.

    PubMed

    Rodionov, M A; Galaktionov, S G; Akhrem, A A

    1987-11-02

    In order to prolong the lifetime of protein bioregulators in blood it is possible to engineer analogs with protected sites of limited proteolysis. To determine the sites, primarily accessible to trypsin-like proteases, a computer procedure has been developed, including a prediction algorithm, to produce the residue diagram of a globular protein and a discriminant algorithm to determine the sites most liable to proteolysis. The accuracy of prediction of amino acid residue exposure is characterised by correlation coefficients between experimental and theoretical exposure values, the coefficients being about 0.7 as calculated for 10 globular proteins. The classification of Arg and Lys residues into two groups, susceptible or insusceptible to protease, has an error percentage of about 25.

  2. Selective observation of the disordered import signal of a globular protein by in-cell NMR: the example of frataxins.

    PubMed

    Popovic, Matija; Sanfelice, Domenico; Pastore, Chiara; Prischi, Filippo; Temussi, Piero Andrea; Pastore, Annalisa

    2015-06-01

    We have exploited the capability of in-cell NMR to selectively observe flexible regions within folded proteins to carry out a comparative study of two members of the highly conserved frataxin family which are found both in prokaryotes and in eukaryotes. They all contain a globular domain which shares more than 50% identity, which in eukaryotes is preceded by an N-terminal tail containing the mitochondrial import signal. We demonstrate that the NMR spectrum of the bacterial ortholog CyaY cannot be observed in the homologous E. coli system, although it becomes fully observable as soon as the cells are lysed. This behavior has been observed for several other compact globular proteins as seems to be the rule rather than the exception. The NMR spectrum of the yeast ortholog Yfh1 contains instead visible signals from the protein. We demonstrate that they correspond to the flexible N-terminal tail indicating that this is flexible and unfolded. This flexibility of the N-terminus agrees with previous studies of human frataxin, despite the extensive sequence diversity of this region in the two proteins. Interestingly, the residues that we observe in in-cell experiments are not visible in the crystal structure of a Yfh1 mutant designed to destabilize the first helix. More importantly, our results show that, in cell, the protein is predominantly present not as an aggregate but as a monomeric species.

  3. Design of a novel globular protein fold with atomic-level accuracy.

    PubMed

    Kuhlman, Brian; Dantas, Gautam; Ireton, Gregory C; Varani, Gabriele; Stoddard, Barry L; Baker, David

    2003-11-21

    A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.

  4. Molecular weight-gyration radius relation of globular proteins: a comparison of light scattering, small-angle X-ray scattering and structure-based data.

    PubMed

    Smilgies, Detlef-M; Folta-Stogniew, Ewa

    2015-10-01

    The molecular weight-gyration radius relation for a number of globular proteins based on experimental light scattering data is compared with small-angle X-ray scattering data recently published by Mylonas & Svergun [J. Appl. Cryst. (2007 ▸), 40, s245-s249]. In addition, other recent experimental data and theoretical calculations are reviewed. It is found that the MW-Rg relation for the globular proteins is well represented by a power law with an exponent of 0.37 (2).

  5. Insight into the Unfolding Properties of Chd64, a Small, Single Domain Protein with a Globular Core and Disordered Tails.

    PubMed

    Tarczewska, Aneta; Kozłowska, Małgorzata; Dobryszycki, Piotr; Kaus-Drobek, Magdalena; Dadlez, Michał; Ożyhar, Andrzej

    2015-01-01

    Two major lipophilic hormones, 20-hydroxyecdysone (20E) and juvenile hormone (JH), govern insect development and growth. While the mode of action of 20E is well understood, some understanding of JH-dependent signalling has been attained only in the past few years, and the crosstalk of the two hormonal pathways remains unknown. Two proteins, the calponin-like Chd64 and immunophilin FKBP39 proteins, have recently been found to play pivotal roles in the formation of dynamic, multiprotein complex that cross-links these two signalling pathways. However, the molecular mechanism of the interaction remains unexplored. The aim of this work was to determine structural elements of Chd64 to provide an understanding of molecular basis of multiple interactions. We analysed Chd64 in two unrelated insect species, Drosophila melanogaster (DmChd64) and Tribolium castaneum (TcChd64). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS), we showed that both Chd64 proteins have disordered tails that outflank the globular core. The folds of the globular cores of both Chd64 resemble the calponin homology (CH) domain previously resolved by crystallography. Monitoring the unfolding of DmChd64 and TcChd64 by far-ultraviolet (UV) circular dichroism (CD) spectroscopy, fluorescence spectroscopy and size-exclusion chromatography (SEC) revealed a highly complex process. Chd64 unfolds and forms of a molten globule (MG)-like intermediate state. Furthermore, our data indicate that in some conditions, Chd64 may exists in discrete structural forms, indicating that the protein is pliable and capable of easily acquiring different conformations. The plasticity of Chd64 and the existence of terminal intrinsically disordered regions (IDRs) may be crucial for multiple interactions with many partners.

  6. Clusters of isoleucine, leucine, and valine side chains define cores of stability in high‐energy states of globular proteins: Sequence determinants of structure and stability

    PubMed Central

    Kathuria, Sagar V.; Chan, Yvonne H.; Nobrega, R. Paul; Özen, Ayşegül

    2015-01-01

    Abstract Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high‐energy states that populate their folding free‐energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high‐energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high‐energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account for the roles of adjacent hydrocarbon moieties in defining stability cores of partially folded states along folding reaction coordinates. PMID:26660714

  7. Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents

    PubMed Central

    King, John T.; Arthur, Evan J.; Brooks, Charles L.; Kubarych, Kevin J.

    2012-01-01

    The thermodynamic driving forces for protein folding, association and function are often determined by protein-water interactions. With a novel covalently bound labeling approach, we have used sensitive vibrational probes, site-selectively conjugated to two lysozyme variants–in conjunction with ultrafast two-dimensional infrared (2D-IR) spectroscopy–to investigate directly the protein-water interface. By probing alternatively a topologically flat, rigid domain and a flexible domain, we find direct experimental evidence for spatially heterogeneous hydration dynamics. The hydration environment around globular proteins can vary from exhibiting bulk-like hydration dynamics to dynamically constrained water, which results from stifled hydrogen bond switching dynamics near extended hydrophobic surfaces. Furthermore, we leverage preferential solvation exchange to demonstrate that the liberation of dynamically constrained water is a sufficient driving force for protein-surface association reactions. These results provide an intuitive picture of the dynamic aspects of hydrophobic hydration of proteins, illustrating an essential function of water in biological processes. PMID:22530969

  8. Detailed abundances for a large sample of giant stars in the globular cluster 47 Tucanae (NGC 104)

    SciTech Connect

    Cordero, M. J.; Pilachowski, C. A.; Johnson, C. I.; McDonald, I.; Zijlstra, A. A.; Simmerer, J. E-mail: catyp@astro.indiana.edu E-mail: mcdonald@jb.man.ac.uk E-mail: jennifer@physics.utah.edu

    2014-01-01

    47 Tuc is an ideal target to study chemical evolution and globular cluster (GC) formation in massive more metal-rich GCs, as it is the closest massive GC. We present chemical abundances for O, Na, Al, Si, Ca, Ti, Fe, Ni, La, and Eu in 164 red giant branch stars in the massive GC 47 Tuc using spectra obtained with both the Hydra multifiber spectrograph at the Blanco 4 m telescope and the FLAMES multiobject spectrograph at the Very Large Telescope. We find an average [Fe/H] = –0.79 ± 0.09 dex, consistent with literature values, as well as overabundances of alpha-elements ([α/Fe] ∼ 0.3 dex). The n-capture process elements indicate that 47 Tuc is r process-dominated ([Eu/La] = +0.24), and the light elements O, Na, and Al exhibit star-to-star variations. The Na-O anticorrelation, a signature typically seen in Galactic GCs, is present in 47 Tuc, and extends to include a small number of stars with [O/Fe] ∼ –0.5. Additionally, the [O/Na] ratios of our sample reveal that the cluster stars can be separated into three distinct populations. A Kolmogorov-Smirnov test demonstrates that the O-poor/Na-rich stars are more centrally concentrated than the O-rich/Na-poor stars. The observed number and radial distribution of 47 Tuc's stellar populations, as distinguished by their light element composition, agrees closely with the results obtained from photometric data. We do not find evidence supporting a strong Na-Al correlation in 47 Tuc, which is consistent with current models of asymptotic giant branch nucleosynthesis yields.

  9. Self-similar assemblies of globular whey proteins at the air-water interface: effect of the structure.

    PubMed

    Mahmoudi, Najet; Gaillard, Cédric; Boué, François; Axelos, Monique A V; Riaublanc, Alain

    2010-05-01

    We investigated the structure of heat-induced assemblies of whey globular proteins using small angle neutron scattering (SANS), static and dynamic light scattering (SLS and DLS), and cryogenic transmission electron microscopy (Cryo-TEM). Whey protein molecules self-assemble in fractal aggregates with a structure density depending on the electrostatic interactions. We determined the static and dynamic properties of interfacial layer formed by the protein assemblies, upon adsorption and spreading at the air-water interface using surface film balance and interfacial dilatational rheology. Upon spreading, all whey protein systems show a power-law scaling behavior of the surface pressure versus concentration in the semi-dilute surface concentration regime, with an exponent ranging from 5.5 to 9 depending on the electrostatic interactions and the aggregation state. The dilatational modulus derived from surface pressure isotherms shows a main peak at 6-8 mN/m, generally considered to be the onset of a conformational change in the monolayer, and a second peak or a shoulder at 15 mN/m. Long-time adsorption kinetics give similar results for both the native whey proteins and the corresponding self-similar assemblies, with a systematic effect of the ionic strength.

  10. BLUE STRAGGLER EVOLUTION CAUGHT IN THE ACT IN THE LARGE MAGELLANIC CLOUD GLOBULAR CLUSTER HODGE 11

    SciTech Connect

    Li Chengyuan; De Grijs, Richard; Liu Xiangkun; Deng Licai E-mail: grijs@pku.edu.cn

    2013-06-10

    High-resolution Hubble Space Telescope imaging observations show that the radial distribution of the field-decontaminated sample of 162 'blue straggler' stars (BSs) in the 11.7{sup +0.2}{sub -0.1} Gyr old Large Magellanic Cloud cluster Hodge 11 exhibits a clear bimodality. In combination with their distinct loci in color-magnitude space, this offers new evidence in support of theoretical expectations that suggest different BS formation channels as a function of stellar density. In the cluster's color-magnitude diagram, the BSs in the inner 15'' (roughly corresponding to the cluster's core radius) are located more closely to the theoretical sequence resulting from stellar collisions, while those in the periphery (at radii between 85'' and 100'') are preferentially found in the region expected to contain objects formed through binary mass transfer or coalescence. In addition, the objects' distribution in color-magnitude space provides us with the rare opportunity in an extragalactic environment to quantify the evolution of the cluster's collisionally induced BS population and the likely period that has elapsed since their formation epoch, which we estimate to have occurred {approx}4-5 Gyr ago.

  11. Blue Straggler Evolution Caught in the Act in the Large Magellanic Cloud Globular Cluster Hodge 11

    NASA Astrophysics Data System (ADS)

    Li, Chengyuan; de Grijs, Richard; Deng, Licai; Liu, Xiangkun

    2013-06-01

    High-resolution Hubble Space Telescope imaging observations show that the radial distribution of the field-decontaminated sample of 162 "blue straggler" stars (BSs) in the 11.7^{+0.2}_{-0.1} Gyr old Large Magellanic Cloud cluster Hodge 11 exhibits a clear bimodality. In combination with their distinct loci in color-magnitude space, this offers new evidence in support of theoretical expectations that suggest different BS formation channels as a function of stellar density. In the cluster's color-magnitude diagram, the BSs in the inner 15'' (roughly corresponding to the cluster's core radius) are located more closely to the theoretical sequence resulting from stellar collisions, while those in the periphery (at radii between 85'' and 100'') are preferentially found in the region expected to contain objects formed through binary mass transfer or coalescence. In addition, the objects' distribution in color-magnitude space provides us with the rare opportunity in an extragalactic environment to quantify the evolution of the cluster's collisionally induced BS population and the likely period that has elapsed since their formation epoch, which we estimate to have occurred ~4-5 Gyr ago.

  12. Biological assessment of neonicotinoids imidacloprid and its major metabolites for potentially human health using globular proteins as a model.

    PubMed

    Ding, Fei; Peng, Wei

    2015-06-01

    The assessment of biological activities of imidacloprid and its two major metabolites, namely 6-chloronicotinic acid and 2-imidazolidone for nontarget organism, by employing essentially functional biomacromolecules, albumin and hemoglobin as a potentially model with the use of circular dichroism (CD), fluorescence, extrinsic 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence as well as molecular modeling is the theme of this work. By dint of CD spectra and synchronous fluorescence, it was clear that the orderly weak interactions between amino acid residues within globular proteins were disturbed by imidacloprid, and this event led to marginally alterations or self-regulations of protein conformation so as to lodge imidacloprid more tightly. Both steady state and time-resolved fluorescence suggested that the fluorescence of Trp residues in proteins was quenched after the presence of imidacloprid, corresponding to noncovalent protein-imidacloprid complexes formation and, the reaction belongs to moderate association (K=1.888/1.614×10(4)M(-1) for albumin/hemoglobin-imidacloprid, respectively), hydrogen bonds and π stacking performed a vital role in stabilizing the complexes, as derived from thermodynamic analysis and molecular modeling. With the aid of hydrophobic ANS experiments, subdomain IIA and α1β2 interface of albumin and hemoglobin, respectively, were found to be preserved high-affinity for imidacloprid. These results ties in with the subsequently molecular modeling laying imidacloprid in the Sudlow's site I and close to Trp-213 residue on albumin, while settling down B/Trp-37 residue nearby in hemoglobin, and these conclusions further confirmed by site-directed mutagenesis and molecular dynamics simulation. But, at the same time, several crucial noncovalent bonds came from other amino acid residues, e.g. Arg-194 and Arg-198 (albumin) and B/Arg-40, B/Asp-99 and B/Asn-102 (hemoglobin) cannot be ignored completely. Based on the comparative studies of

  13. Proteolytic activities of kiwifruit actinidin (Actinidia deliciosa cv. Hayward) on different fibrous and globular proteins: a comparative study of actinidin with papain.

    PubMed

    Chalabi, Maryam; Khademi, Fatemeh; Yarani, Reza; Mostafaie, Ali

    2014-04-01

    Actinidin, a member of the papain-like family of cysteine proteases, is abundant in kiwifruit. To date, a few studies have been provided to investigate the proteolytic activity and substrate specificity of actinidin on native proteins. Herein, the proteolytic activity of actinidin was compared to papain on several different fibrous and globular proteins under neutral, acidic and basic conditions. The digested samples were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and densitometry to assess the proteolytic effect. Furthermore, the levels of free amino nitrogen (FAN) of the treated samples were determined using the ninhydrin colorimetric method. The findings showed that actinidin has no or limited proteolytic effect on globular proteins such as immunoglobulins including sheep IgG, rabbit IgG, chicken IgY and fish IgM, bovine serum albumin (BSA), lipid transfer protein (LTP), and whey proteins (α-lactalbumin and β-lactoglobulin) compared to papain. In contrast to globular proteins, actinidin could hydrolyze collagen and fibrinogen perfectly at neutral and mild basic pHs. Moreover, this enzyme could digest pure α-casein and major subunits of micellar casein especially in acidic pHs. Taken together, the data indicated that actinidin has narrow substrate specificity with the highest enzymatic activity for the collagen and fibrinogen substrates. The results describe the actinidin as a mild plant protease useful for many special applications such as cell isolation from different tissues and some food industries as a mixture formula with other relevant proteases.

  14. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.

    PubMed

    Ferreira, Diogo C; van der Linden, Marx G; de Oliveira, Leandro C; Onuchic, José N; de Araújo, Antônio F Pereira

    2016-04-01

    Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations.

  15. A Very Large Array Search for Intermediate-mass Black Holes in Globular Clusters in M81

    NASA Astrophysics Data System (ADS)

    Wrobel, J. M.; Miller-Jones, J. C. A.; Middleton, M. J.

    2016-07-01

    Nantais et al. used the Hubble Space Telescope to localize probable globular clusters (GCs) in M81, a spiral galaxy at a distance of 3.63 Mpc. Theory predicts that GCs can host intermediate-mass black holes (IMBHs) with masses {M}{{BH}}˜ 100{--}{100,000} {M}⊙ . Finding IMBHs in GCs could validate a formation channel for seed BHs in the early universe, bolster gravitational-wave predictions for space missions, and test scaling relations between stellar systems and the central BHs they host. We used the NRAO Karl G. Jansky Very Large Array to search for the radiative signatures of IMBH accretion from 206 probable GCs in a mosaic of M81. The observing wavelength was 5.5 cm, and the spatial resolution was 1.″5 (26.4 pc). None of the individual GCs are detected, nor are weighted-mean image stacks of the 206 GCs and the 49 massive GCs with stellar masses {M}\\star ≳ {200,000} {M}⊙ . We apply a semiempirical model to predict the mass of an IMBH that, if undergoing accretion in the long-lived, hard X-ray state, is consistent with a given radio luminosity. The 3σ radio-luminosity upper limits correspond to IMBH masses of \\overline{{M}{{BH}}({{all}})}\\lt {42,000}\\quad {M}⊙ for the all-cluster stack and \\overline{{M}{{BH}}({{massive}})}\\lt {51,000}\\quad {M}⊙ for the massive-cluster stack. We also apply the empirical fundamental-plane relation to two X-ray-detected clusters, finding that their individual IMBH masses at 95% confidence are M BH < 99,000 M ⊙ and {M}{{BH}}\\lt {15,000} {M}⊙ . Finally, no analog of HLX-1, a strong IMBH candidate in an extragalactic star cluster, occurs in any individual GC in M81. This underscores the uniqueness or rarity of the HLX-1 phenomenon.

  16. Protein selectivity with immobilized metal ion-tacn sorbents: chromatographic studies with human serum proteins and several other globular proteins.

    PubMed

    Jiang, W; Graham, B; Spiccia, L; Hearn, M T

    1998-01-01

    The chromatographic selectivity of the immobilized chelate system, 1,4,7-triazocyclononane (tacn), complexed with the borderline metal ions Cu2+, Cr3+, Mn2+, Co2+, Zn2+, and Ni2+ has been investigated with hen egg white lysozyme, horse heart cytochrome c, and horse skeletal muscle myoglobin, as well as proteins present in partially fractionated preparations of human plasma. The effects of ionic strength and pH of the loading and elution buffers on protein selectivities of these new immobilized metal ion affinity chromatographic (IMAC) systems have been examined. The results confirm that immobilized Mn;pl-tacn sorbents exhibit a novel type of IMAC behavior with proteins. In particular, the chromatographic properties of these immobilized M(n+)-tacn ligand systems were significantly different compared to the IMAC behavior observed with other types of immobilized tri- and tetradentate chelating ligands, such as iminodiacetic acid, O-phosphoserine, or nitrilotriacetic acid, when complexed with borderline metal ions. The experimental results have consequently been evaluated in terms of the additional contributions to the interactive processes mediated by effects other than solely the conventional lone pair Lewis soft acid-Lewis soft base coordination interactions, typically found for the IMAC of proteins with borderline and soft metal ions, such as Cu2+ or Ni2+.

  17. Acrylonitrile quenching of trp phosphorescence in proteins: a probe of the internal flexibility of the globular fold.

    PubMed

    Strambini, Giovanni B; Gonnelli, Margherita

    2010-08-04

    Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O(2) and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) =k(0) exp[-(r -r(0))/r(e)], with an attenuation length r(e) = 0.03 nm and a contact rate k(0) = 3.6 x 10(10) s(-1). At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 x 10(9) M(-1)s(-1) for free Trp in water, in proteins kq ranged from 6.5 x 10(6) M(-1)s(-1) for superficial sites to 1.3 x 10(2) M(-1)s(-1) for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.

  18. Probing the binding behavior and conformational states of globular proteins in reversed-phase high-performance liquid chromatography.

    PubMed

    Purcell, A W; Aguilar, M I; Hearn, M T

    1999-07-01

    that these proteins can undergo via molten globule-like intermediates (i.e., compact denatured states with a significant amount of residual secondary structure) in solution has also been examined. This study thus further documents an experimental strategy to assess the folding/unfolding behavior of globular proteins in the presence of hydrophobic surfaces and aquo-organic solvents, whereby the system parameters can potentially affect the preservation of native conformations, and thus the function, of the protein under these conditions.

  19. Exploration of the origin and evolution of globular proteins by mRNA display.

    PubMed

    Yanagawa, Hiroshi

    2013-06-04

    The questions of how proteins first appeared on the primitive earth and how they evolved into functional proteins are fundamental. If we can understand the origins and evolution of proteins, we should be able to create novel functional proteins. Evolutionary protein engineering or directed protein evolution has been used to create artificial proteins with novel functions by repeated mutation, selection, and amplification, mimicking Darwinian evolution in the laboratory. For this purpose, display technology, such as mRNA display, to link genotype with phenotype is extremely important. Here I focus on three hypotheses regarding the origin and evolution of proteins. First, Eigen's GNC hypothesis proposes that the early genetic code began from the directionless codons GNC and GNN, where N denotes U, C, A, or G. Second, Ohno's gene duplication theory proposes that gene duplication produces two functionally redundant, paralogous genes, of which one retains the original function, leaving the second free to evolve adaptively. Third, Gilbert's exon shuffling theory proposes that new genes are formed through shuffling of small segments corresponding to exons. I then review various experimental approaches to evolutionary protein engineering using mRNA display, such as the creation of functional proteins from random sequences with limited sets of amino acids, randomly mutated folded proteins, and block-shuffled sequence proteins, and I discuss the results in relation to these three hypotheses.

  20. iHADAMAC: A complementary tool for sequential resonance assignment of globular and highly disordered proteins

    NASA Astrophysics Data System (ADS)

    Feuerstein, Sophie; Plevin, Michael J.; Willbold, Dieter; Brutscher, Bernhard

    2012-01-01

    An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing the 1H- 15N correlations into seven different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard encoding scheme based on four different spin manipulations as recently introduced in the context of the sequential HADAMAC experiment. Both sequential and intra-residue HADAMAC experiments yield highly complementary information that greatly facilitate resonance assignment of proteins with high frequency degeneracy, as demonstrated here for a 188-residue intrinsically disordered protein fragment of the hepatitis C virus protein NS5A.

  1. Spider Gland Fluids: From Protein-Rich Isotropic Liquid to Insoluble Super Fiber

    DTIC Science & Technology

    2013-09-17

    proteins regardless of their large molecular weights (200 - 350 kDa). One can estimate the expected rotational correlation time of a globular ...radius of the hydration shell. If the silk proteins were folded globular proteins, we estimate a correlation time of 84 µs for a 300 kDa silk protein...for the different residues, overall these long relaxation times are typically observed for globular proteins that are an order of magnitude smaller

  2. Role of local and nonlocal interactions in folding and misfolding of globular proteins

    NASA Astrophysics Data System (ADS)

    Kumar, Adesh; Baruah, Anupaul; Biswas, Parbati

    2017-02-01

    A Monte Carlo simulation based sequence design method is proposed to study the role of the local and the nonlocal interactions with varying secondary structure content in protein folding, misfolding and unfolding. A statistical potential is developed from the compilation of a data set of proteins, which accounts for the respective contribution of local and the nonlocal interactions. Sequences are designed through a combination of positive and negative design by a Monte Carlo simulation in the sequence space. The weights of the local and the nonlocal interactions are tuned appropriately to study the role of the local and the nonlocal interactions in the folding, unfolding and misfolding of the designed sequences. Results suggest that the nonlocal interactions are the primary determinant of protein folding while the local interactions may be required but not always necessary. The nonlocal interactions mainly guide the polypeptide chain to form compact structures but do not differentiate between the native-like conformations, while the local interactions stabilize the target conformation against the native-like competing conformations. The study concludes that the local interactions govern the fold-misfold transition, while the nonlocal interactions regulate the fold-unfold transition of proteins. However, for proteins with predominantly β-sheet content, the nonlocal interactions control both fold-misfold and fold-unfold transitions.

  3. Stokes-flow computation of the diffusion coefficient and rotational diffusion tensor of lysozyme, a globular protein

    NASA Astrophysics Data System (ADS)

    Zhao, Hong; Pearlstein, Arne J.

    2002-07-01

    Based on a closed surface of triangles fitted to atomic coordinates determined crystallographically, Brune and Kim [Proc. Natl. Acad. Sci. USA 90, 3835-3839 (1993)] proposed a boundary-element Stokes-flow technique for ab initio computation of a translational diffusion coefficient and the rotational diffusion tensor Dr of globular proteins. They applied their approach to atomic coordinates for a tetragonal structure of hen egg-white lysozyme, and reported that computed values of a translational diffusion coefficient and Dr=tr(Dr)/3 agreed well with experiment. After establishing the identity between the infinite-dilution tracer diffusion coefficient of the protein macroion (D+ for lysozyme cation) and the "translational diffusion coefficient" computed by Brune and Kim, we adopt a somewhat different computational approach and show how convergence of D+ and Dr for tetragonal lysozyme depends on two computational parameters characterizing the fidelity of the geometric approximation to the protein surface and two others characterizing the accuracy of the Stokes-flow computations. We then compute D+ and Dr for lysozyme using atomic coordinates for the triclinic crystal structure, three structures determined by nuclear magnetic resonance spectroscopy in the liquid phase (presumably corresponding more closely to in vivo structures), the solvated tetragonal structure (with 108 water molecules) considered by Brune and Kim, and a "dry" version of the same structure. These computations show that D+ and Dr computed for all of the dry crystal structures are in excellent agreement with those for the liquid-phase conformations. Values of D+ and Dr computed for the solvated structure are lower, consistent with the larger volume and area of the corresponding polyhedral surface. We also show that several choices of the origin of the force system [discussed by Brenner, J. Colloid Interface Sci. 23, 407-436 (1967)] give rise to nearly identical translational diffusion coefficients

  4. X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins.

    PubMed

    Baral, Pravas Kumar; Swayampakula, Mridula; Aguzzi, Adriano; James, Michael N G

    2015-10-01

    Misfolded prion proteins are the cause of neurodegenerative diseases that affect many mammalian species, including humans. Transmission of the prion diseases poses a considerable public-health risk as a specific prion disease such as bovine spongiform encephalopathy can be transferred to humans and other mammalian species upon contaminant exposure. The underlying mechanism of prion propagation and the species barriers that control cross species transmission has been investigated quite extensively. So far a number of prion strains have been characterized and those have been intimately linked to species-specific infectivity and other pathophysiological manifestations. These strains are encoded by a protein-only agent, and have a high degree of sequence identity across mammalian species. The molecular events that lead to strain differentiation remain elusive. In order to contribute to the understanding of strain differentiation, we have determined the crystal structures of the globular, folded domains of four prion proteins (cow, deer, elk and Syrian hamster) bound to the POM1 antibody fragment Fab. Although the overall structural folds of the mammalian prion proteins remains extremely similar, there are several local structural variations observed in the misfolding-initiator motifs. In additional molecular dynamics simulation studies on these several prion proteins reveal differences in the local fluctuations and imply that these differences have possible roles in the unfolding of the globular domains. These local variations in the structured domains perpetuate diverse patterns of prion misfolding and possibly facilitate the strain selection and adaptation.

  5. Self crowding of globular proteins studied by small-angle x-ray scattering.

    PubMed

    Goldenberg, David P; Argyle, Brian

    2014-02-18

    Small-angle x-ray scattering (SAXS) was used to study the behavior of equine metmyoglobin (Mb) and bovine pancreatic trypsin inhibitor (BPTI) at concentrations up to 0.4 and 0.15 g/mL, respectively, in solutions also containing 50% D2O and 1 M urea. For both proteins, significant effects because of interference between x-rays scattered by different molecules (interparticle interference) were observed, indicating nonideal behavior at high concentrations. The experimental data were analyzed by comparison of the observed scattering profiles with those predicted by crystal structures of the proteins and a hard-sphere fluid model used to represent steric exclusion effects. The Mb scattering data were well fit by the hard-sphere model using a sphere radius of 18 Å, only slightly smaller than that estimated from the three-dimensional structure (20 Å). In contrast, the scattering profiles for BPTI in phosphate buffer displayed substantially less pronounced interparticle interference than predicted by the hard-sphere model and the radius estimated from the known structure of the protein (15 Å). Replacing the phosphate buffer with 3-(N-morpolino)propane sulfonic acid (MOPS) led to increased interparticle interference, consistent with a larger effective radius and suggesting that phosphate ions may mediate attractive intermolecular interactions, as observed in some BPTI crystal structures, without the formation of stable oligomers. The scattering data were also used to estimate second virial coefficients for the two proteins: 2.0 ×10(-4) cm(3)mol/g(2) for Mb in phosphate buffer, 1.6 ×10(-4) cm(3)mol/g(2) for BPTI in phosphate buffer and 9.2 ×10(-4) cm(3)mol/g(2) for BPTI in MOPS. The results indicate that the behavior of Mb, which is nearly isoelectric under the conditions used, is well described by the hard-sphere model, but that of BPTI is considerably more complex and is likely influenced by both repulsive and attractive electrostatic interactions. The hard

  6. Self Crowding of Globular Proteins Studied by Small-Angle X-Ray Scattering

    PubMed Central

    Goldenberg, David P.; Argyle, Brian

    2014-01-01

    Small-angle x-ray scattering (SAXS) was used to study the behavior of equine metmyoglobin (Mb) and bovine pancreatic trypsin inhibitor (BPTI) at concentrations up to 0.4 and 0.15 g/mL, respectively, in solutions also containing 50% D2O and 1 M urea. For both proteins, significant effects because of interference between x-rays scattered by different molecules (interparticle interference) were observed, indicating nonideal behavior at high concentrations. The experimental data were analyzed by comparison of the observed scattering profiles with those predicted by crystal structures of the proteins and a hard-sphere fluid model used to represent steric exclusion effects. The Mb scattering data were well fit by the hard-sphere model using a sphere radius of 18 Å, only slightly smaller than that estimated from the three-dimensional structure (20 Å). In contrast, the scattering profiles for BPTI in phosphate buffer displayed substantially less pronounced interparticle interference than predicted by the hard-sphere model and the radius estimated from the known structure of the protein (15 Å). Replacing the phosphate buffer with 3-(N-morpolino)propane sulfonic acid (MOPS) led to increased interparticle interference, consistent with a larger effective radius and suggesting that phosphate ions may mediate attractive intermolecular interactions, as observed in some BPTI crystal structures, without the formation of stable oligomers. The scattering data were also used to estimate second virial coefficients for the two proteins: 2.0 ×10-4 cm3mol/g2 for Mb in phosphate buffer, 1.6 ×10-4 cm3mol/g2 for BPTI in phosphate buffer and 9.2 ×10-4 cm3mol/g2 for BPTI in MOPS. The results indicate that the behavior of Mb, which is nearly isoelectric under the conditions used, is well described by the hard-sphere model, but that of BPTI is considerably more complex and is likely influenced by both repulsive and attractive electrostatic interactions. The hard-sphere model may be

  7. Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution

    DOE PAGES

    Grimaldo, Marco; Roosen-Runge, Felix; Hennig, Marcus; ...

    2015-06-17

    The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs= 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchymore » particles. In conclusion, the finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.« less

  8. The crystal structure of the streptococcal collagen-like protein 2 globular domain from invasive M3-type group A Streptococcus shows significant similarity to immunomodulatory HIV protein gp41.

    PubMed

    Squeglia, Flavia; Bachert, Beth; De Simone, Alfonso; Lukomski, Slawomir; Berisio, Rita

    2014-02-21

    The arsenal of virulence factors deployed by streptococci includes streptococcal collagen-like (Scl) proteins. These proteins, which are characterized by a globular domain and a collagen-like domain, play key roles in host adhesion, host immune defense evasion, and biofilm formation. In this work, we demonstrate that the Scl2.3 protein is expressed on the surface of invasive M3-type strain MGAS315 of Streptococcus pyogenes. We report the crystal structure of Scl2.3 globular domain, the first of any Scl. This structure shows a novel fold among collagen trimerization domains of either bacterial or human origin. Despite there being low sequence identity, we observed that Scl2.3 globular domain structurally resembles the gp41 subunit of the envelope glycoprotein from human immunodeficiency virus type 1, an essential subunit for viral fusion to human T cells. We combined crystallographic data with modeling and molecular dynamics techniques to gather information on the entire lollipop-like Scl2.3 structure. Molecular dynamics data evidence a high flexibility of Scl2.3 with remarkable interdomain motions that are likely instrumental to the protein biological function in mediating adhesive or immune-modulatory functions in host-pathogen interactions. Altogether, our results provide molecular tools for the understanding of Scl-mediated streptococcal pathogenesis and important structural insights for the future design of small molecular inhibitors of streptococcal invasion.

  9. Where Are the Universe's Globular Clusters?

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-04-01

    Observations of globular clusters gravitationally-bound, spherical clusters of stars that orbit galaxies as satellites are critical to studies of galactic and stellar evolution. What type of galaxies host the largest total number of globular clusters in todays universe? A recent study answers this question.Total number of globular clusters vs. host galaxy luminosity for a catalog of ~400 galaxies of all types. [Harris 2016]Globular FavoritismGlobular clusters can be found in the halos of all galaxies above a critical brightness of about 107 solar luminosities (in practice, all but the smallest of dwarfs). The number of globulars a galaxy hosts is related to its luminosity: the Milky Way is host to ~150 globulars, the slightly brighterAndromeda galaxy may have several hundred globulars, and the extremelybright giant elliptical galaxy M87 likely has over ten thousand.But the number of galaxies is not evenly distributed in luminosity; tiny dwarf galaxies are extremely numerous in the universe, whereas giant ellipticals are far less common. So are most of the universes globulars found around dwarfs, simply because there are more dwarfs to host them? Or are the majority ofglobular clusters orbiting large galaxies? A scientist at McMaster University in Canada, William Harris, has done some calculations to find the answer.Finding the PeakHarris combines two components in his estimates:The Schechter function, a function that describes the relative number of galaxies per unit luminosity. This function drops off near a characteristic luminosity roughly that of our galaxy.Empirical data from ~400 galaxies that describe the average number of globulars per galaxy as a function of galaxy luminosity.Relative number of globular clusters in all galaxies at a given luminosity, for metal-poor globulars only (blue), metal-rich globulars only (red), and all globulars (black). The curves peak around the Schechter characteristic luminosity, and metal-poor globulars outnumber metal

  10. Roles of the highly conserved amino acids in the globular head and stalk region of the Newcastle disease virus HN protein in the membrane fusion process.

    PubMed

    Sun, Chengxi; Wen, Hongling; Chen, Yuzhen; Chu, Fulu; Lin, Bin; Ren, Guijie; Song, Yanyan; Wang, Zhiyu

    2015-02-01

    Newcastle disease virus (NDV), an avain paramyxovirus, has been assigned to the genus Avulavirus within the family Paramyxoviridae. It causes Newcastle disease (ND) that is a highly contagious and fatal viral disease affecting poultry and most species of birds. The hemagglutinin-neuraminidase (HN) protein of NDV has multiple functions including mediating hemadsorption (HAD), neuraminidase (NA), and fusion promotion activities affecting the process of viral attachment, entry, replication and dissemination. Fusion ability of the NDV was highly correlated to its virulence. Mutations in the HN globular head and headless HN of NDV were constructed to determinate the impact of highly conserved amino acids in the globular head of paramyxovirus HN proteins and the roles of the stalk region of HN in the fusion process. It was found that the interaction between F and HN mutants E401A, G402A, G468A, V469A, Y526A, and T527A was equal to that in F and wt HN. The mutations of G402A, G468A, V469A, and T527A had various effects on cell fusion promotion, receptor binding ability, and NA activity, but the membrane merging rate was comparable to wt HN. The elimination of hemadsorption ability and NA activity of E401A and Y526A resulted in the loss of the fusion promotion function of HN. The conclusion was that receptor binding and NA had a common active site and E401 and Y526 amino acids were essential for virus attachment, entry, and dissemination. In addition, G468A mutation made different contributions to HAD and NA, which indicated that G468 was one of the potential key amino acids in switching the two functions between receptor binding and sialic acid destruction of HN. It was also proven that the headless HN of NDV could promote the fusion event mediated by F. Thus, it revealed a novel mechanism in F activation of NDV.

  11. The different molar absorptivities of the secondary structure types in the amide I region: an attenuated total reflection infrared study on globular proteins.

    PubMed

    de Jongh, H H; Goormaghtigh, E; Ruysschaert, J M

    1996-11-01

    Differences in molar absorptivity of the various secondary structures in the amide I region of infrared protein spectra would have a great impact on the interpretation of the data published thus far on protein films studied by attenuated total reflection infrared spectroscopy. In this work, representative values for amide I absorptivities are obtained for 15 different films of globular proteins spread from H2O solutions. The observed intensities are corrected for variations in film thickness and for contributions of hydration water, atmospheric water, and side chains. These absorptivities, together with the reported secondary structure of the proteins investigated, are used to deduce the molar absorptivities of the individual secondary structure types. It is found that the molar absorptivity of beta-strands is 1.4-1.6 times larger than that of alpha-helices, which in turn is 1.3-2.1 times larger than those found for beta-turns or random coiled structures. The implications of our findings for spectral analysis currently used in literature are discussed.

  12. Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution

    SciTech Connect

    Grimaldo, Marco; Roosen-Runge, Felix; Hennig, Marcus; Zanini, Fabio; Zhang, Fajun; Zamponi, Michaela; Jalarvo, Niina; Schreiber, Frank; Seydel, Tilo

    2015-06-17

    The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs= 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. In conclusion, the finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.

  13. Fluorescence behavior of globular proteins from their bulk and thin film conformations in presence of mono-, di- and tri-valent ions.

    PubMed

    Bhowal, Ashim Chandra; Das, Kaushik; Kundu, Sarathi

    2015-09-01

    Photoluminescence behavior of globular proteins, lysozyme and bovine serum albumin (BSA), from their bulk and thin film conformations have been studied in presence of mono-, di- and tri-valent ions by using fluorescence and UV-Vis spectroscopy at two different temperatures and the morphology of the protein thin films have been studied by using atomic force microscopy. Protein- and ion-dependent dynamic and static quenching behaviors have been identified. While dynamic quenching is observed for lysozyme for all the three different valent ions, BSA shows no quenching for mono-valent (Na(+)) ions, dynamic quenching for di-valent (Ni(2+)) ions and static quenching for tri-valent (Fe(3+)) ions at pH≈5.5. After heat treatment, as the conformation of the protein molecules changes, the quenching efficiency for lysozyme in presence of ions decreases but shows enhancement for BSA. In thin film geometry, the molecular conformation of both lysozyme and BSA modifies on the solid surfaces and hence quenching efficiency also modifies in comparison with that of bulk and as a result the quenching efficiency for lysozyme increases but decreases for the BSA film.

  14. The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation

    PubMed Central

    Rogala, Kacper B; Dynes, Nicola J; Hatzopoulos, Georgios N; Yan, Jun; Pong, Sheng Kai; Robinson, Carol V; Deane, Charlotte M; Gönczy, Pierre; Vakonakis, Ioannis

    2015-01-01

    Centrioles are microtubule-based organelles crucial for cell division, sensing and motility. In Caenorhabditis elegans, the onset of centriole formation requires notably the proteins SAS-5 and SAS-6, which have functional equivalents across eukaryotic evolution. Whereas the molecular architecture of SAS-6 and its role in initiating centriole formation are well understood, the mechanisms by which SAS-5 and its relatives function is unclear. Here, we combine biophysical and structural analysis to uncover the architecture of SAS-5 and examine its functional implications in vivo. Our work reveals that two distinct self-associating domains are necessary to form higher-order oligomers of SAS-5: a trimeric coiled coil and a novel globular dimeric Implico domain. Disruption of either domain leads to centriole duplication failure in worm embryos, indicating that large SAS-5 assemblies are necessary for function in vivo. DOI: http://dx.doi.org/10.7554/eLife.07410.001 PMID:26023830

  15. The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation.

    PubMed

    Rogala, Kacper B; Dynes, Nicola J; Hatzopoulos, Georgios N; Yan, Jun; Pong, Sheng Kai; Robinson, Carol V; Deane, Charlotte M; Gönczy, Pierre; Vakonakis, Ioannis

    2015-05-29

    Centrioles are microtubule-based organelles crucial for cell division, sensing and motility. In Caenorhabditis elegans, the onset of centriole formation requires notably the proteins SAS-5 and SAS-6, which have functional equivalents across eukaryotic evolution. Whereas the molecular architecture of SAS-6 and its role in initiating centriole formation are well understood, the mechanisms by which SAS-5 and its relatives function is unclear. Here, we combine biophysical and structural analysis to uncover the architecture of SAS-5 and examine its functional implications in vivo. Our work reveals that two distinct self-associating domains are necessary to form higher-order oligomers of SAS-5: a trimeric coiled coil and a novel globular dimeric Implico domain. Disruption of either domain leads to centriole duplication failure in worm embryos, indicating that large SAS-5 assemblies are necessary for function in vivo.

  16. Detergent pretreatment of solid phase globular proteins in ELISA`s. Enhanced antigenicity and subsequent sensitivity. Final report, September 1989-September 1991

    SciTech Connect

    Blanchard, G.C.; Bouhmadouche, M.; Williamson, M.L.

    1994-10-01

    Methods for pretreatment and rejuvenation of preimmobilized globular proteins used in immunodiagnostics were investigated using reagents routinely used in ELISA`s. Rabbit and goat gamma globulins, functioning as antigens, and antibodies on non-covalent, and covalent solid surfaces, were monitored for detergent mediated desorption, denaturation, non-specific binding and altered antigenicity. The results from fourteen commercially supplied polyvinyl- and polystyrene-derivatized microtiter plates coated with antibody or antigenic lgG were compared with commercial microtiter diagnostic plates with preimmobilized lgG. Wash solutions had no effect on immobilized gamma globulins when the solid phase protein functioned as an antibody on covalent or noncovalent surfaces. In addition to tween 20 removing up to 50% of noncovalently bound protein additional binding sites are apparently exposed on solid phase antigens, evident by an increase in signal, which cannot be explained by nonspecific binding. However, no increase in signal was evident when antigen was preimmobilized covalently. The role of between 20 and other reagent components in ELISA-based assays are explored. The screening of noncovalent preimmobilized antigen coated surfaces prior to use for deteraent mediated enhancement is suggested.

  17. Complement Protein C1q Interacts with DC-SIGN via Its Globular Domain and Thus May Interfere with HIV-1 Transmission

    PubMed Central

    Pednekar, Lina; Pandit, Hrishikesh; Paudyal, Basudev; Kaur, Anuvinder; Al-Mozaini, Maha Ahmed; Kouser, Lubna; Ghebrehiwet, Berhane; Mitchell, Daniel A.; Madan, Taruna; Kishore, Uday

    2016-01-01

    Dendritic cells (DCs) are the most potent antigen-presenting cells capable of priming naïve T-cells. Its C-type lectin receptor, DC-SIGN, regulates a wide range of immune functions. Along with its role in HIV-1 pathogenesis through complement opsonization of the virus, DC-SIGN has recently emerged as an adaptor for complement protein C1q on the surface of immature DCs via a trimeric complex involving gC1qR, a receptor for the globular domain of C1q. Here, we have examined the nature of interaction between C1q and DC-SIGN in terms of domain localization, and implications of C1q–DC-SIGN-gC1qR complex formation on HIV-1 transmission. We first expressed and purified recombinant extracellular domains of DC-SIGN and its homologue DC-SIGNR as tetramers comprising of the entire extra cellular domain including the α-helical neck region and monomers comprising of the carbohydrate recognition domain only. Direct binding studies revealed that both DC-SIGN and DC-SIGNR were able to bind independently to the recombinant globular head modules ghA, ghB, and ghC, with ghB being the preferential binder. C1q appeared to interact with DC-SIGN or DC-SIGNR in a manner similar to IgG. Mutational analysis using single amino acid substitutions within the globular head modules showed that TyrB175 and LysB136 were critical for the C1q–DC-SIGN/DC-SIGNR interaction. Competitive studies revealed that gC1qR and ghB shared overlapping binding sites on DC-SIGN, implying that HIV-1 transmission by DCs could be modulated due to the interplay of gC1qR-C1q with DC-SIGN. Since C1q, gC1qR, and DC-SIGN can individually bind HIV-1, we examined how C1q and gC1qR modulated HIV-1–DC-SIGN interaction in an infection assay. Here, we report, for the first time, that C1q suppressed DC-SIGN-mediated transfer of HIV-1 to activated pooled peripheral blood mononuclear cells, although the globular head modules did not. The protective effect of C1q was negated by the addition of gC1qR. In fact, gC1qR enhanced

  18. Complement Protein C1q Interacts with DC-SIGN via Its Globular Domain and Thus May Interfere with HIV-1 Transmission.

    PubMed

    Pednekar, Lina; Pandit, Hrishikesh; Paudyal, Basudev; Kaur, Anuvinder; Al-Mozaini, Maha Ahmed; Kouser, Lubna; Ghebrehiwet, Berhane; Mitchell, Daniel A; Madan, Taruna; Kishore, Uday

    2016-01-01

    Dendritic cells (DCs) are the most potent antigen-presenting cells capable of priming naïve T-cells. Its C-type lectin receptor, DC-SIGN, regulates a wide range of immune functions. Along with its role in HIV-1 pathogenesis through complement opsonization of the virus, DC-SIGN has recently emerged as an adaptor for complement protein C1q on the surface of immature DCs via a trimeric complex involving gC1qR, a receptor for the globular domain of C1q. Here, we have examined the nature of interaction between C1q and DC-SIGN in terms of domain localization, and implications of C1q-DC-SIGN-gC1qR complex formation on HIV-1 transmission. We first expressed and purified recombinant extracellular domains of DC-SIGN and its homologue DC-SIGNR as tetramers comprising of the entire extra cellular domain including the α-helical neck region and monomers comprising of the carbohydrate recognition domain only. Direct binding studies revealed that both DC-SIGN and DC-SIGNR were able to bind independently to the recombinant globular head modules ghA, ghB, and ghC, with ghB being the preferential binder. C1q appeared to interact with DC-SIGN or DC-SIGNR in a manner similar to IgG. Mutational analysis using single amino acid substitutions within the globular head modules showed that Tyr(B175) and Lys(B136) were critical for the C1q-DC-SIGN/DC-SIGNR interaction. Competitive studies revealed that gC1qR and ghB shared overlapping binding sites on DC-SIGN, implying that HIV-1 transmission by DCs could be modulated due to the interplay of gC1qR-C1q with DC-SIGN. Since C1q, gC1qR, and DC-SIGN can individually bind HIV-1, we examined how C1q and gC1qR modulated HIV-1-DC-SIGN interaction in an infection assay. Here, we report, for the first time, that C1q suppressed DC-SIGN-mediated transfer of HIV-1 to activated pooled peripheral blood mononuclear cells, although the globular head modules did not. The protective effect of C1q was negated by the addition of gC1qR. In fact, gC1qR enhanced DC

  19. Gamma-ray Emission from Globular Clusters

    NASA Astrophysics Data System (ADS)

    Tam, Pak-Hin T.; Hui, Chung Y.; Kong, Albert K. H.

    2016-03-01

    Over the last few years, the data obtained using the Large Area Telescope (LAT) aboard the Fermi Gamma-ray Space Telescope has provided new insights on high-energy processes in globular clusters, particularly those involving compact objects such as MilliSecond Pulsars (MSPs). Gamma-ray emission in the 100 MeV to 10 GeV range has been detected from more than a dozen globular clusters in our galaxy, including 47 Tucanae and Terzan 5. Based on a sample of known gammaray globular clusters, the empirical relations between gamma-ray luminosity and properties of globular clusters such as their stellar encounter rate, metallicity, and possible optical and infrared photon energy densities, have been derived. The measured gamma-ray spectra are generally described by a power law with a cut-off at a few gigaelectronvolts. Together with the detection of pulsed γ-rays from two MSPs in two different globular clusters, such spectral signature lends support to the hypothesis that γ-rays from globular clusters represent collective curvature emission from magnetospheres of MSPs in the clusters. Alternative models, involving Inverse-Compton (IC) emission of relativistic electrons that are accelerated close to MSPs or pulsar wind nebula shocks, have also been suggested. Observations at >100 GeV by using Fermi/LAT and atmospheric Cherenkov telescopes such as H.E.S.S.-II, MAGIC-II, VERITAS, and CTA will help to settle some questions unanswered by current data.

  20. Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins.

    PubMed

    O'Brien, Edward P; Brooks, Bernard R; Thirumalai, D

    2009-05-05

    Experiments show that for many two-state folders the free energy of the native state, DeltaG(ND)([C]), changes linearly as the denaturant concentration, [C], is varied. The slope {m = [dDeltaG(ND)([C])]/(d[C])}, is nearly constant. According to the transfer model, the m-value is associated with the difference in the surface area between the native (N) and denatured (D) state, which should be a function of DeltaR(g)(2), the difference in the square of the radius of gyration between the D and N states. Single-molecule experiments show that the R(g) of the structurally heterogeneous denatured state undergoes an equilibrium collapse transition as [C] decreases, which implies m also should be [C]-dependent. We resolve the conundrum between constant m-values and [C]-dependent changes in R(g) using molecular simulations of a coarse-grained representation of protein L, and the molecular transfer model, for which the equilibrium folding can be accurately calculated as a function of denaturant (urea) concentration. In agreement with experiment, we find that over a large range of denaturant concentration (>3 M) the m-value is a constant, whereas under strongly renaturing conditions (<3 M), it depends on [C]. The m-value is a constant above [C] > 3 M because the [C]-dependent changes in the surface area of the backbone groups, which make the largest contribution to m, are relatively narrow in the denatured state. The burial of the backbone and hydrophobic side chains gives rise to substantial surface area changes below [C] < 3 M, leading to collapse in the denatured state of protein L. Dissection of the contribution of various amino acids to the total surface area change with [C] shows that both the sequence context and residual structure are important. There are [C]-dependent variations in the surface area for chemically identical groups such as the backbone or Ala. Consequently, the midpoints of transition of individual residues vary significantly (which we call the Holtzer

  1. Identity of the core proteins of the large chondroitin sulphate proteoglycans synthesized by skeletal muscle and prechondrogenic mesenchyme.

    PubMed Central

    Carrino, D A; Dennis, J E; Drushel, R F; Haynesworth, S E; Caplan, A I

    1994-01-01

    Large, chondroitin sulphate-containing proteoglycans are synthesized by three prominent tissue in the embryonic chick limb. One of these proteoglycans is aggrecan, the phenotype-specific proteoglycan of cartilage. Another, PG-M, is produced by prechondrogenic mesenchymal cells. The third, M-CSPG, is made by developing skeletal muscle cells. While the carbohydrate components of PG-M and M-CSPG share some similarities, both of these proteoglycans clearly have different carbohydrate moieties from those of aggrecan. To compare these three proteoglycans at another level, their core protein structures were analysed in three ways: by the presence or absence of monoclonal antibody epitopes, by one-dimensional peptide display of the cyanogen bromide-cleaved core proteins and by electron microscopic imaging of the molecules. Monoclonal antibodies whose epitopes are present in aggrecan core protein were tested with core protein preparations from M-CSPG and PG-M. One of these, 7D1, recognizes both PG-M and M-CSPG, while another, 1C6, shows no reactivity for the non-cartilage proteoglycans. The absence of 1C6 reactivity is of interest, as its epitope is in a region of the aggrecan core protein known to have a functional homologue in the core proteins of PG-M and M-CSPG. The cyanogen bromide-fragmented peptide pattern of M-CSPG is the same as that of PG-M, and both are different from that of aggrecan. The aggrecan pattern has one prominent large band (molecular mass 130 kDa), some less prominent large bands (molecular mass 70-100 kDa) and several smaller bands. In contrast, the PG-M and M-CSPG patterns show no bands with molecular masses > 73 kDa, and the smaller bands (molecular mass < 40 kDa) have a different pattern to that of the smaller bands from aggrecan. The electron microscopic images of aggrecan show a core protein with one end having two globular regions separated by a short linear segment; adjacent to this is a long linear segment, which sometimes contains a third

  2. Stellar black holes in globular clusters

    NASA Technical Reports Server (NTRS)

    Kulkarni, S. R.; Hut, Piet; Mcmillan, Steve

    1993-01-01

    The recent discovery of large populations of millisec pulsars associated with neutron stars in globular clusters indicates that several hundred stellar black holes of about 10 solar masses each can form within a typical cluster. While, in clusters of high central density, the rapid dynamical evolution of the black-hole population leads to an ejection of nearly all holes on a short timescale, systems of intermediate density may involve a normal star's capture by one of the surviving holes to form a low-mass X-ray binary. One or more such binaries may be found in the globular clusters surrounding our galaxy.

  3. From coiled coils to small globular proteins: design of a native-like three-helix bundle.

    PubMed Central

    Bryson, J. W.; Desjarlais, J. R.; Handel, T. M.; DeGrado, W. F.

    1998-01-01

    A monomolecular native-like three-helix bundle has been designed in an iterative process, beginning with a peptide that noncooperatively assembled into an antiparallel three-helix bundle. Three versions of the protein were designed in which specific interactions were incrementally added. The hydrodynamic and spectroscopic properties of the proteins were examined by size exclusion chromatography, sedimentation equilibrium, fluorescence spectroscopy, and NMR. The thermodynamics of folding were evaluated by monitoring the thermal and guanidine-induced unfolding transitions using far UV circular dichroism spectroscopy. The attainment of a unique, native-like state was achieved through the introduction of: (1) helix capping interactions; (2) electrostatic interactions between partially exposed charged residues; (3) a diverse collection of apolar side chains within the hydrophobic core. PMID:9655345

  4. Chemical abundances of multiple stellar populations in massive globular clusters

    NASA Astrophysics Data System (ADS)

    Marino, Anna F.

    2017-03-01

    Multiple stellar populations in the Milky Way globular clusters manifest themselves with a large variety. Although chemical abundance variations in light elements, including He, are ubiquitous, the amount of these variations is different in different globulars. Stellar populations with distinct Fe, C+N+O and slow-neutron capture elements have been now detected in some globular clusters, whose number will likely increase. All these chemical features correspond to specific photometric patterns. I review the chemical+photometric features of the multiple stellar populations in globular clusters and discuss how the interpretation of data is being more and more challenging. Very excitingly, the origin and evolution of globular clusters is being a complex puzzle to compose.

  5. The non-uniform early structural response of globular proteins to cold denaturing conditions: A case study with Yfh1

    SciTech Connect

    Chatterjee, Prathit; Bagchi, Sayan E-mail: s.bagchi@ncl.res.in; Sengupta, Neelanjana E-mail: s.bagchi@ncl.res.in

    2014-11-28

    The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (T{sub s}), and the experimentally observed temperature of complete unfolding, 268 K (T{sub c}). Within the simulated timescales, discernible “global” level structural loss at T{sub c} is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at T{sub c} in comparison to T{sub s}. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at T{sub c}. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at T{sub c} due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.

  6. The soluble recombinant form of a binding protein/receptor for the globular domain of C1q (gC1qR) enhances blood coagulation.

    PubMed

    Peerschke, E I; Jesty, J; Reid, K B; Ghebrehiwet, B

    1998-01-01

    The gC1qR is a ubiquitously expressed, 33 kDa cellular protein which recognizes the globular domains of C1q. Recent evidence suggests that the gC1qR also serves as the Zn(++)-dependent endothelial cell binding site for factor XII and high-molecular-weight kininogen, and activates intrinsic coagulation and kinin pathways in purified systems. In addition, activated lymphocytes have been reported to release soluble gC1qR. Thus, the present study investigated the procoagulant potential of soluble gC1qR in human plasma using the recombinant protein (rgC1qR). rgC1qR supported a dose-dependent shortening of extrinsic coagulation using the prothrombin time in the presence of diluted (1/50-1/500) thromboplastin. Maximum enhancement of the prothrombin time resulted in shortening of the clotting time from 78.8 +/- 0.4 s to 68.5 +/- 0.6 s (mean +/- SD, n = 8) in the presence of 50 micrograms/ml (1.5 mumol/l) rgC1qR. rgC1qR also enhanced the intrinsic pathway of coagulation evaluated in the absence of activators of the contact system, as demonstrated by a shortening of the plasma recalcification time from 348 +/- 66 s to 140 +/- 23 s (n = 4). rgC1qR, however, had no effect on intrinsic coagulation in the presence of undiluted kaolin or ellagic acid, and under these conditions failed to shorten the activated partial thromboplastin time of factor VIII or factor-IX-deficient plasma. rgC1qR further failed to affect thrombin and factor Xa generation assayed using chromogenic substrates, and did not enhance thrombin-induced conversion of fibrinogen to fibrin. Interestingly, the procoagulant activity of the rgC1qR was measurable in either factor-XII- or factor-XI-deficient plasma, suggesting that it was not exclusively focused on the contact system of coagulation. Although the mechanism of action of gC1qR on blood coagulation remains obscure, the data suggest a potential role for this protein in hemostatic and thrombotic events.

  7. Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?

    PubMed Central

    Baker, Nathan A.; McCammon, J. Andrew

    2008-01-01

    The solvent reaction field potential of an uncharged protein immersed in Simple Point Charge/Extended (SPC/E) explicit solvent was computed over a series of molecular dynamics trajectories, intotal 1560 ns of simulation time. A finite, positive potential of 13 to 24 kbTec−1 (where T = 300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 Å from the solute surface, on average 0.008 ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit-solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. PMID:17949217

  8. Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa.

    PubMed

    Wallnoefer, Hannes G; Handschuh, Sandra; Liedl, Klaus R; Fox, Thomas

    2010-06-03

    The role of water molecules is increasingly attracting attention in structural biology, and many studies have demonstrated their crucial contribution to the stability and function of proteins. Here, we present molecular dynamics studies on factor Xa (fXa) to investigate the effect of water molecules in this serine protease. fXa is a key enzyme in the blood coagulation cascade, and thus, an important target for antithrombotic drugs. A reasonable representation of the structure is crucial for an investigation at the molecular level and, thus, a prerequisite for structure-based drug design. Simulations of well-resolved fXa X-ray structures with different sets of water molecules show the importance of a well-determined water set for the simulation. We discuss implications of different water sets on the structure and dynamics of fXa.

  9. Binaries in globular clusters

    NASA Technical Reports Server (NTRS)

    Hut, Piet; Mcmillan, Steve; Goodman, Jeremy; Mateo, Mario; Phinney, E. S.; Pryor, Carlton; Richer, Harvey B.; Verbunt, Frank; Weinberg, Martin

    1992-01-01

    Recent observations have shown that globular clusters contain a substantial number of binaries most of which are believed to be primordial. We discuss different successful optical search techniques, based on radial-velocity variables, photometric variables, and the positions of stars in the color-magnitude diagram. In addition, we review searches in other wavelengths, which have turned up low-mass X-ray binaries and more recently a variety of radio pulsars. On the theoretical side, we give an overview of the different physical mechanisms through which individual binaries evolve. We discuss the various simulation techniques which recently have been employed to study the effects of a primordial binary population, and the fascinating interplay between stellar evolution and stellar dynamics which drives globular-cluster evolution.

  10. Synthesis of globular precursors.

    PubMed

    Teixidor, Francesc; Sillanpää, Reijo; Pepiol, Ariadna; Lupu, Marius; Viñas, Clara

    2015-09-01

    o-Carborane (C2 B10 H12 ) was adapted to perform as the core of globular macromolecules, dendrons or dendrimers. To meet this objective, precisely defined substitution patterns of terminal olefin groups on the carborane framework were subjected to Heck cross-coupling reactions or hydroboration leading to hydroxyl terminated arms. These led to new terminal groups (chloro, bromo, and tosyl leaving groups, organic acid, and azide) that permitted ester production, click chemistry, and oxonium ring opening to be performed as examples of reactions that demonstrate the wide possibilities of the globular icosahedral carboranes to produce new dendritic or dendrimer-like structures. Polyanionic species were obtained in high yield through the ring-opening reaction of cyclic oxonium compound [3,3'-Co(8-C4 H8 O2 -1,2-C2 B9 H10 )(1',2'-C2 B9 H11 )] by using terminal hydroxyl groups as nucleophiles. These new polyanionic compounds that contain multiple metallacarborane clusters at their periphery may prove useful as new classes of compounds for boron neutron capture therapy with enhanced water solubility and as cores to make a new class of high-boron globular macromolecules.

  11. Quantification of particle sizes with metal replication under standard freeze-etching conditions: a gold ball standard for calibrating shadow widths was used to measure freeze-etched globular proteins.

    PubMed

    Ruben, G C

    1995-11-01

    120 sec yielded a low contrast, less granular Pt-C film. Both gold balls and protein particles were subjected in separate experiments to either 19 or 120 sec of outgassing of the Pt-C gun prior to Pt-C replication. Outgassing had a profound effect on the average size of the Pt-C shadow widths on both gold and protein particles. The Pt-C gun outgassing procedure also determined the smallest replicated particle that could be resolved. The frequency of some smaller gold ball sizes detected after replication was reduced disproportionately with 19 sec vs. 120 sec outgassing. However, Pt-C gun outgassing did not affect the average measured diameter of the Pt-C-coated protein particles. The "geometric assumption" that each metal-coated particle creates a shadow width the same size as the metal-coated particle diameter was tested using a globular protein. Pt-C replication of protein particles at a 45 degree and 20 degree angle could not confirm the geometric assumption because an average shadow width was always significantly larger than its average Pt-C-coated particle diameter. A model for how the large shadow widths are formed is presented. Gold balls were also replicated at a 45 degree angle with current high resolution conditions at a substrate temperature of -185 degrees C, and the results of these replicas were compared to the results reported here at approximately -100 degrees C.

  12. Super-resolution fluorescence of huntingtin reveals growth of globular species into short fibers and coexistence of distinct aggregates.

    PubMed

    Duim, Whitney C; Jiang, Yan; Shen, Koning; Frydman, Judith; Moerner, W E

    2014-12-19

    Polyglutamine-expanded huntingtin, the protein encoded by HTT mutations associated with Huntington's disease, forms aggregate species in vitro and in vivo. Elucidation of the mechanism of growth of fibrillar aggregates from soluble monomeric protein is critical to understanding the progression of Huntington's disease and to designing therapeutics for the disease, as well as for aggregates implicated in Alzheimer's and Parkinson's diseases. We used the technique of multicolor single-molecule, super-resolution fluorescence imaging to characterize the growth of huntingtin exon 1 aggregates. The huntingtin exon 1 aggregation followed a pathway from exclusively spherical or globular species of ∼80 nm to fibers ∼1 μm in length that increased in width, but not length, over time with the addition of more huntingtin monomers. The fibers further aggregated with one another into aggregate assemblies of increasing size. Seeds created by sonication, which were comparable in shape and size to the globular species in the pathway, were observed to grow through multidirectional elongation into fibers, suggesting a mechanism for growth of globular species into fibers. The single-molecule sensitivity of our approach made it possible to characterize the aggregation pathway across a large range of size scales, from monomers to fiber assemblies, and revealed the coexistence of different aggregate species (globular species, fibers, fiber assemblies) even at late time points.

  13. A large-scale evaluation of computational protein function prediction.

    PubMed

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

  14. A large-scale evaluation of computational protein function prediction

    PubMed Central

    Radivojac, Predrag; Clark, Wyatt T; Ronnen Oron, Tal; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Böhm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-01-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools. PMID:23353650

  15. Adenovirus dodecahedron allows large multimeric protein transduction in human cells.

    PubMed

    Fender, P; Schoehn, G; Foucaud-Gamen, J; Gout, E; Garcel, A; Drouet, E; Chroboczek, J

    2003-04-01

    Adenovirus dodecahedron is a virus-like particle composed of only two viral proteins of human adenovirus serotype 3 that are responsible for virus attachment and internalization. We show here that this dodecameric particle, devoid of genetic information, efficiently penetrates human cells and can deliver large multimeric proteins such as immunoglobulins.

  16. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

    PubMed

    Brannan, Kristopher W; Jin, Wenhao; Huelga, Stephanie C; Banks, Charles A S; Gilmore, Joshua M; Florens, Laurence; Washburn, Michael P; Van Nostrand, Eric L; Pratt, Gabriel A; Schwinn, Marie K; Daniels, Danette L; Yeo, Gene W

    2016-10-20

    RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.

  17. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2007-09-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  18. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2014-07-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  19. The galactic globular cluster system

    NASA Technical Reports Server (NTRS)

    Djorgovski, S.; Meylan, G.

    1994-01-01

    We explore correlations between various properties of Galactic globular clusters, using a database on 143 objects. Our goal is identify correlations and trends which can be used to test and constrain theoretical models of cluster formation and evolution. We use a set of 13 cluster parameters, 9 of which are independently measured. Several arguments suggest that the number of clusters still missing in the obscured regions of the Galaxy is of the order of 10, and thus the selection effects are probably not severe for our sample. Known clusters follow a power-law density distribution with a slope approximately -3.5 to -4, and an apparent core with a core radius approximately 1 kpc. Clusters show a large dynamical range in many of their properties, more so for the core parameters (which are presumably more affected by dynamical evolution) than for the half-light parameters. There are no good correlations with luminosity, although more luminous clusters tend to be more concentrated. When data are binned in luminosity, several trends emerge: more luminous clusters tend to have smaller and denser cores. We interpret this as a differential survival effect, with more massive clusters surviving longer and reaching more evolved dynamical states. Cluster core parameters and concentrations also correlate with the position in the Galaxy, with clusters closer to the Galactic center or plane being more concentrated and having smaller and denser cores. These trends are more pronounced for the fainter (less massive) clusters. This is in agreement with a picture where tidal shocks form disk or bulge passages accelerate dynamical evolution of clusters. Cluster metallicities do not correlate with any other parameter, including luminosity and velocity dispersion; the only detectable trend is with the position in the Galaxy, probably reflecting Zinn's disk-halo dichotomy. This suggests that globular clusters were not self-enriched systems. Velocity dispersions show excellent correlations

  20. Globular Clusters as Cradles of Life and Advanced Civilizations

    NASA Astrophysics Data System (ADS)

    Di Stefano, R.; Ray, A.

    2016-08-01

    Globular clusters are ancient stellar populations in compact dense ellipsoids. There is no star formation and there are no core-collapse supernovae, but several lines of evidence suggest that globular clusters are rich in planets. If so, and if advanced civilizations can develop there, then the distances between these civilizations and other stars would be far smaller than typical distances between stars in the Galactic disk, facilitating interstellar communication and travel. The potent combination of long-term stability and high stellar densities provides a globular cluster opportunity. Yet the very proximity that promotes interstellar travel also brings danger, as stellar interactions can destroy planetary systems. We find, however, that large portions of many globular clusters are “sweet spots,” where habitable-zone planetary orbits are stable for long times. Globular clusters in our own and other galaxies are, therefore, among the best targets for searches for extraterrestrial intelligence (SETI). We use the Drake equation to compare the likelihood of advanced civilizations in globular clusters to that in the Galactic disk. We also consider free-floating planets, since wide-orbit planets can be ejected to travel through the cluster. Civilizations spawned in globular clusters may be able to establish self-sustaining outposts, reducing the probability that a single catastrophic event will destroy the civilization. Although individual civilizations may follow different evolutionary paths, or even be destroyed, the cluster may continue to host advanced civilizations once a small number have jumped across interstellar space. Civilizations residing in globular clusters could therefore, in a sense, be immortal.

  1. The Nature of LSB galaxies revealed by their Globular Clusters

    NASA Astrophysics Data System (ADS)

    Kissler-Patig, Markus

    2005-07-01

    Low Surface Brightness {LSB} galaxies encompass many of the extremes in galaxy properties. Their understanding is essential to complete our picture of galaxy formation and evolution. Due to their historical under-representation on galaxy surveys, their importance to many areas of astronomy has only recently began to be realized. Globular clusters are superb tracers of the formation histories of galaxies and have been extensively used as such in high surface brightness galaxies. We propose to investigate the nature of massive LSB galaxies by studying their globular cluster systems. No globular cluster study has been reported for LSB galaxies to date. Yet, both the presence or absence of globular clusters set very strong constraints on the conditions prevailing during LSB galaxy formation and evolution. Both in dwarf and giant high surface brightness {HSB} galaxies, globular clusters are known to form as a constant fraction of baryonic mass. Their presence/absence immediately indicates similarities or discrepancies in the formation and evolution conditions of LSB and HSB galaxies. In particular, the presence/absence of metal-poor halo globular clusters infers similarities/differences in the halo formation and assembly processes of LSB vs. HSB galaxies, while the presence/absence of metal-rich globular clusters can be used to derive the occurrence and frequency of violent events {such as mergers} in the LSB galaxy assembly history. Two band imaging with ACS will allow us to identify the globular clusters {just resolved at the selected distance} and to determine their metallicity {potentially their rough age}. The composition of the systems will be compared to the extensive census built up on HSB galaxies. Our representative sample of six LSB galaxies {cz < 2700 km/s} are selected such, that a large system of globular clusters is expected. Globular clusters will constrain phases of LSB galaxy formation and evolution that can currently not be probed by other means. HST

  2. Optics of globular photonic crystals

    SciTech Connect

    Gorelik, V S

    2007-05-31

    The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter {approx}200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported. (review)

  3. Globular clusters with Gaia

    NASA Astrophysics Data System (ADS)

    Pancino, E.; Bellazzini, M.; Giuffrida, G.; Marinoni, S.

    2017-01-01

    The treatment of crowded fields in Gaia data will only be a reality in a few years from now. In particular, for globular clusters, only the end-of-mission data (public in 2022-2023) will have the necessary full crowding treatment and will reach sufficient quality for the faintest stars. As a consequence, the work on the deblending and decontamination pipelines is still ongoing. We describe the present status of the pipelines for different Gaia instruments, and we model the end-of-mission crowding errors on the basis of available information. We then apply the nominal post-launch Gaia performances, appropriately worsened by the estimated crowding errors, to a set of 18 simulated globular clusters with different concentration, distance, and field contamination. We conclude that there will be 103-104 stars with astrometric performances virtually untouched by crowding (contaminated by <1 mmag) in the majoritiy of clusters. The most limiting factor will be field crowding, not cluster crowding: the most contaminated clusters will only contain 10-100 clean stars. We also conclude that: (i) the systemic proper motions and parallaxes will be determined to 1% or better up to ≃15 kpc, and the nearby clusters will have radial velocities to a few km s-1 ; (ii) internal kinematics will be of unprecendented quality, cluster masses will be determined to ≃10% up to 15 kpc and beyond, and it will be possible to identify differences of a few km s-1 or less in the kinematics (if any) of cluster sub-populations up to 10 kpc and beyond; (iii) the brightest stars (V≃17 mag) will have space-quality, wide-field photometry (mmag errors), and all Gaia photometry will have 1-3% errors on the absolute photometric calibration.

  4. Formation of globular clusters with multiple populations

    NASA Astrophysics Data System (ADS)

    Decressin, T.

    2017-03-01

    Spectroscopic and photometric evidences have led to a complete revision of our understanding of globular clusters with the discovery of multiple stellar populations which differ chemically. Whereas some stars have a chemical composition similar to fields stars, others show large star-to-star variations in light elements (Li to Al) while their composition in iron and heavy elements stay constant. This peculiar chemical pattern can be explained by self-pollution of the intracluster gas occurring in the early evolution of clusters. Here the possible impact from a first generation of fast rotating stars to the early evolution of globular clusters is presented. The high rotation velocity will allow the stars to rotate at the break-up velocity and release matter enrich in H-burning which in turn will produce new stars with a chemical composition in agreement with observations. The massive stars have also an important role to clear the cluster from the remaining gas left after the star formation episodes. If the gas expulsion is fast enough, the strong change in the potential well will lead to the loss of stars occupying the outer part of the cluster. As second generation stars are preferentially born in the cluster centre, the ratio of second to first generation stars will increase over time to match the present ratio determined by observations. Considerations on the properties of low-mass stars still present in globular clusters will also be presented.

  5. Pythoscape: a framework for generation of large protein similarity networks.

    PubMed

    Barber, Alan E; Babbitt, Patricia C

    2012-11-01

    Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence-structure-function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.

  6. Relativistic Binaries in Globular Clusters.

    PubMed

    Benacquista, Matthew J; Downing, Jonathan M B

    2013-01-01

    Galactic globular clusters are old, dense star systems typically containing 10(4)-10(6) stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution that leads to relativistic binaries, and current and possible future observational evidence for this population. Our discussion of globular cluster evolution will focus on the processes that boost the production of tight binary systems and the subsequent interaction of these binaries that can alter the properties of both bodies and can lead to exotic objects. Direct N-body integrations and Fokker-Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.

  7. Large-Scale Measurement of Absolute Protein Glycosylation Stoichiometry.

    PubMed

    Sun, Shisheng; Zhang, Hui

    2015-07-07

    Protein glycosylation is one of the most important protein modifications. Glycosylation site occupancy alteration has been implicated in human diseases and cancers. However, current glycoproteomic methods focus on the identification and quantification of glycosylated peptides and glycosylation sites but not glycosylation occupancy or glycoform stoichiometry. Here we describe a method for large-scale determination of the absolute glycosylation stoichiometry using three independent relative ratios. Using this method, we determined 117 absolute N-glycosylation occupancies in OVCAR-3 cells. Finally, we investigated the possible functions and the determinants for partial glycosylation.

  8. Strategies for crystallization of large membrane protein complexes

    NASA Astrophysics Data System (ADS)

    Yoshikawa, Shinya; Shinzawa-Itoh, Kyoko; Ueda, Hidefumi; Tsukihara, Tomitake; Fukumoto, Yoshihisa; Kubota, Tomomi; Kawamoto, Masahide; Fukuyama, Keiichi; Matsubara, Hiroshi

    1992-08-01

    Crystalline cytochrome c oxidase and ubiquinol: cytochrome c oxidoreductase which diffracted X-rays at 7-8A˚resolution were obtained from bovine heart mitochondria. The methods for the purification and crystallization of these enzymes indicate that large membrane protein complexes are easier to purify and crystallize than smaller homologous membrane protein complexes, because the former have more hydrophilic surface than the latter. Bulky and polydispersed detergents such as Brij-35 and Tween 20 attached to the isolated complex are not always obstructive to crystallization if they are effective for stabilizing the complexes.

  9. Inhibition of smooth muscle cell proliferation by adiponectin requires proteolytic conversion to its globular form.

    PubMed

    Fuerst, Melissa; Taylor, Carla G; Wright, Brenda; Tworek, Leslee; Zahradka, Peter

    2012-10-01

    Accelerated atherosclerosis is the primary cardiovascular manifestation of diabetes and correlates inversely with levels of circulating adiponectin, an anti-atherosclerotic adipokine that declines in diabetes. We therefore initiated a study to examine the mechanisms by which adiponectin, a hormone released from adipose tissue, influences the proliferation of vascular smooth muscle cells (SMCs). Addition of adiponectin to quiescent porcine coronary artery SMCs increased both protein and DNA synthesis and concurrently activated ERK1/2 and Akt. By contrast, globular adiponectin, a truncated form of this protein, exhibited anti-mitogenic properties as indicated by the inhibition of protein and DNA synthesis in SMCs stimulated with platelet-derived growth factor (PDGF). Whereas globular adiponectin did not stimulate growth-related signal transduction pathways, it was able to block the PDGF-dependent phosphorylation of eukaryotic elongation factor 2 kinase, a regulator of protein synthesis. Proteolysis of adiponectin with trypsin, which produces globular adiponectin, reversed the growth-stimulating actions of the undigested protein. As the existence of globular adiponectin remains controversial, western blotting was used to establish its presence in rat serum. We found that globular adiponectin was detectable in rat serum, but this result was not obtained with all antibodies. The contrasting properties of adiponectin and its globular form with respect to SMC proliferation suggest that protection against atherosclerosis may therefore be mediated, in part, by the level of globular adiponectin.

  10. Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

    PubMed

    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.

  11. Comprehensive functional analysis of large lists of genes and proteins.

    PubMed

    Mlecnik, Bernhard; Galon, Jérôme; Bindea, Gabriela

    2017-03-22

    The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis. Results are visualized as networks in which Gene Ontology (GO) terms and pathways are grouped based on their biological role. Many species are now supported by ClueGO and additional organisms are added on demand. ClueGO can be used together with the CluePedia App to enable the visualization of protein-protein interactions within or between pathways.

  12. Tools for Interpreting Large-Scale Protein Profiling in Microbiology

    PubMed Central

    Hendrickson, E. L.; Lamont, R. J.; Hackett, M.

    2009-01-01

    Quantitative proteome analysis of microbial systems generates large datasets that can be difficult and time consuming to interpret. Fortunately, many of the data display and gene clustering tools developed to analyze large transcriptome microarray datasets are also applicable to proteomes. Plots of abundance ratio versus total signal or spectral counts can highlight regions of random error and putative change. Displaying data in the physical order of the genes in the genome sequence can highlight potential operons. At a basic level of transcriptional organization, identifying operons can give insights into regulatory pathways as well as provide corroborating evidence for proteomic results. Classification and clustering algorithms can group proteins together by their abundance changes under different conditions, helping to identify interesting expression patterns, but often work poorly with noisy data like that typically generated in a large-scale proteome analysis. Biological interpretation can be aided more directly by overlaying differential protein abundance data onto metabolic pathways, indicating pathways with altered activities. More broadly, ontology tools detect altered levels of protein abundance for different metabolic pathways, molecular functions and cellular localizations. In practice, pathway analysis and ontology are limited by the level of database curation associated with the organism of interest. PMID:18946006

  13. A structural dissection of large protein-protein crystal packing contacts.

    PubMed

    Luo, Jiesi; Liu, Zhongyu; Guo, Yanzhi; Li, Menglong

    2015-09-15

    With the rapid increase in crystal structures of protein-protein complexes deposited in the Protein Data Bank (PDB), more and more crystal contacts have been shown to have similar or even larger interface areas than biological interfaces. However, little attention has been paid to these large crystal packing contacts and their structural principles remain unknown. To address this issue, we used a comparative feature analysis to analyze the geometric and physicochemical properties of large crystal packing contacts by comparing two types of specific protein-protein interactions (PPIs), weak transient complexes and permanent homodimers. Our results show that although large crystal packing contacts have a similar interface area and contact size as permanent homodimers, they tend to be more planar, loosely packed and less hydrophobic than permanent homodimers and cannot form a central core region that is fully buried during interaction. However, the properties of large crystal packing contacts, except for the interface area and contact size, more closely resemble those of weak transient complexes. The large overlap between biological and large crystal packing contacts indicates that interface properties are not efficient indicators for classification of biological interfaces from large crystal packing contacts and finding other specific features urgently needed.

  14. Keck spectroscopy and NGVS photometry in the direction of the Virgo cluster: Globular cluster satellites of dwarf ellipticals, Milky Way halo substructure, and large-scale structure in the background

    NASA Astrophysics Data System (ADS)

    Muller, Meredith; Toloba, E.; Guhathakurta, P.; Yagati, S.; Chen, J.; Cote, P.; Dorman, C.; Ferrarese, L.; Peng, E. W.; Next Generation Virgo Cluster Survey Collaboration

    2014-01-01

    The Virgo cluster, the nearest large galaxy cluster, is a rich repository of dwarf elliptical (dE) galaxies. The formation mechanism of dE galaxies remains the subject of much debate. Dwarf galaxies in general are believed to be building blocks in the hierarchical growth of galaxies as per the “cold dark matter” model of structure formation. Globular cluster (GC) satellites serve as important tracers of dark matter in the outer regions of dEs (beyond 1 half-light radius). This project presents new spectroscopic data from Keck's DEIMOS, which specifically targeted low-luminosity (-17 < Mv < -15) dEs and GC satellites, in the Virgo cluster. These data are among the deepest spectroscopic data ever taken in this region. Secondary science targets - Milky Way foreground stars and galaxies in the background - are also discussed. All targets were chosen based on photometric data from the Next Generation Virgo Survey (NGVS) and the Advanced Camera for Surveys Virgo Cluster Survey (ACSVCS). Further, these two surveys were critical to the tomographic analysis of spectroscopic targets. From this analysis we were able to: identify 117 GCs associated with any one of the 21 dE targets in the Virgo cluster, identify Milky Way foreground stars as part of the Virgo Overdensity or Sagittarius streams, quantify the velocity structure of these ongoing cannibalism events, and identify two new superclusters of galaxies in the background using redshift distribution. This research was carried out under the auspices of UCSC's Science Internship Program. We thank the National Science Foundation for funding support. ET was supported by a Fulbright fellowship.

  15. VARIABLE STARS IN THE LARGE MAGELLANIC CLOUD GLOBULAR CLUSTER NGC 2257. I. RESULTS BASED ON 2007-2008 B, V PHOTOMETRY

    SciTech Connect

    Nemec, James M.; Walker, Alistair; Jeon, Young-Beom E-mail: awalker@ctio.edu

    2009-11-15

    The variable stars in the Large Magellanic Cloud star cluster NGC 2257 are reinvestigated using photometry (to {approx}20th mag) of over 400 new B, V CCD images taken with the CTIO 0.9 m telescope on 14 nights in 2007 December and 2008 January. New period searches have been made using two independent algorithms (CLEAN, Period04); the resultant periods of most of the stars are consistent with the pulsation periods derived previously, and where there are discrepancies these have been resolved. For the B and V light curves, accurate Fourier coefficients and parameters are given. Six new variable stars have been discovered (V45-50), including a bright candidate long-period variable star showing secondary oscillations (V45) and two anomalously bright RRc stars (V48 and V50), which are shown to be brightened and reddened by nearby red giant stars. Also discovered among the previously known variable stars are three double-mode RR Lyrae stars (V8, V16, and V34) and several Blazhko variables. Archival Hubble Space Telescope images and the photometry by Johnson et al. have been used to define better the properties of the most crowded variable stars. The total number of cluster variable stars now stands at forty-seven: 23 RRab stars, four of which show Blazhko amplitude variations; 20 RRc stars, one showing clear Blazhko variations and another showing possible Blazhko variations; the three RRd stars, all having the dominant period {approx}0.36 day and period ratios P {sub 1}/P {sub 0} {approx}0.7450; and an LPV star located near the tip of the red giant branch. A comparison of the RRd stars with those in other environments shows them to be most similar to those in IC4499.

  16. Shape-dependent global deformation modes of large protein structures

    NASA Astrophysics Data System (ADS)

    Miloshevsky, Gennady V.; Hassanein, Ahmed; Jordan, Peter C.

    2010-05-01

    Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT Aa proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT Aa biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following and its simplification using a rotation-translation of protein blocks (RTB), are described and applied to gain insight into the nature of gating transitions in gA and KcsA. These studies demonstrate the severe limitations of standard NMA in characterizing the structural rearrangements associated with gating transitions. Comparison of all-atom and RTB transition pathways in gA clearly illustrates the impact of the rigid protein block approximation and the need to include all degrees of freedom and their relaxation in computational studies of protein gating. The effects of atomic level structure, pH, hydrogen bonding and charged residues on the large-scale conformational changes associated with gating transitions are discussed.

  17. Pulsating White Dwarfs in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Kanaan, A.; Zabot, A.; Fraga, L.

    2012-09-01

    We present our current efforts to detect pulsating white dwarfs in globular clusters and analyze the future of this area when the Extremely Large Telescope (ELT), the Giant Magellan Telescope (GMT) and the Thirty-Meter Telescope (TMT) all become operational. Today we are able to detect pulsating white dwarfs in M 4, NGC 6397 and NGC 6752. When ELT comes on line we should be able to improve the quality of data for the nearby clusters and push the limit to at least 3 magnitudes further, up to NGC 6626, increasing the number of observable clusters from 3 to 20.

  18. The Globular cluster system of M31.

    NASA Astrophysics Data System (ADS)

    Galleti, S.; Buzzoni, A.; Federici, L.; Fusi Pecci, F.

    I present here some results of the extensive revision work of M31 confirmed and candidate globular clusters. The Revised Bologna Catalog, RBC, www.bo.astro.it/M31 is currently the largest and most complete database available online. Two spectroscopic surveys are in progress to confirm RBC cluster candidates as well as newly identified candidates at large distances from the center of M31. I have also studied a subsample of bright and young (age < 2 Gyr) clusters in M31 that doesn't appear to have any counterpart in the Milky Way.

  19. Predicting protein functions from redundancies in large-scale protein interaction networks

    NASA Technical Reports Server (NTRS)

    Samanta, Manoj Pratim; Liang, Shoudan

    2003-01-01

    Interpreting data from large-scale protein interaction experiments has been a challenging task because of the widespread presence of random false positives. Here, we present a network-based statistical algorithm that overcomes this difficulty and allows us to derive functions of unannotated proteins from large-scale interaction data. Our algorithm uses the insight that if two proteins share significantly larger number of common interaction partners than random, they have close functional associations. Analysis of publicly available data from Saccharomyces cerevisiae reveals >2,800 reliable functional associations, 29% of which involve at least one unannotated protein. By further analyzing these associations, we derive tentative functions for 81 unannotated proteins with high certainty. Our method is not overly sensitive to the false positives present in the data. Even after adding 50% randomly generated interactions to the measured data set, we are able to recover almost all (approximately 89%) of the original associations.

  20. Sizing Large Proteins and Protein Complexes by Electrospray Ionization Mass Spectrometry and Ion Mobility

    PubMed Central

    Kaddis, Catherine S.; Lomeli, Shirley H.; Yin, Sheng; Berhane, Beniam; Apostol, Marcin I.; Kickhoefer, Valerie A.; Rome, Leonard H.; Loo, Joseph A.

    2009-01-01

    Mass spectrometry (MS) and ion mobility with electrospray ionization (ESI) have the capability to measure and detect large noncovalent protein-ligand and protein-protein complexes. Using an ion mobility method termed GEMMA (Gas-Phase Electrophoretic Mobility Molecular Analysis), protein particles representing a range of sizes can be separated by their electrophoretic mobility in air. Highly charged particles produced from a protein complex solution using electrospray can be manipulated to produce singly charged ions which can be separated and quantified by their electrophoretic mobility. Results from ESI-GEMMA analysis from our laboratory and others were compared to other experimental and theoretically determined parameters, such as molecular mass and cryoelectron microscopy and x-ray crystal structure dimensions. There is a strong correlation between the electrophoretic mobility diameter determined from GEMMA analysis and the molecular mass for protein complexes up to 12 MDa, including the 93 kDa enolase dimer, the 480 kDa ferritin 24-mer complex, the 4.6 MDa cowpea chlorotic mottle virus (CCMV), and the 9 MDa MVP-vault assembly. ESI-GEMMA is used to differentiate a number of similarly sized vault complexes that are composed of different N-terminal protein tags on the MVP subunit. The average effective density of the proteins and protein complexes studied was 0.6 g/cm3. Moreover, there is evidence that proteins and protein complexes collapse or become more compact in the gas phase in the absence of water. PMID:17434746

  1. RR Lyrae stars in M31 globular clusters: B514

    NASA Astrophysics Data System (ADS)

    Contreras, R.; Federici, L.; Clementini, G.; Cacciari, C.; Merighi, R.; Kinemuchi, K.; Catelan, M.; Fusi Pecci, F.; Marconi, M.; Pritzl, B.; Smith, H.

    We present preliminary results of a variable star search in the metal-poor globular cluster B514 of the Andromeda galaxy (M31), based on Hubble Space Telescope Wide Field Planetary Camera 2 and Advanced Camera for Surveys observations. A large number of RR Lyrae stars have been identified for the first time in a globular cluster of M31. The average period of the RR Lyrae variables (< Pab > = 0.58 days and < Pc > = 0.35 days, for fundamental-mode and first-overtone pulsators, respectively) and the position in the period-amplitude diagram both suggest that B514 is likely an Oosterhoff I cluster, contrary to the general behaviour of the metal-poor globular clusters in the Milky Way, which show instead Oosterhoff type II pulsation properties.

  2. Detecting differential protein expression in large-scale population proteomics

    SciTech Connect

    Ryu, Soyoung; Qian, Weijun; Camp, David G.; Smith, Richard D.; Tompkins, Ronald G.; Davis, Ronald W.; Xiao, Wenzhong

    2014-06-17

    Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

  3. Monomeric red fluorescent proteins with a large Stokes shift.

    PubMed

    Piatkevich, Kiryl D; Hulit, James; Subach, Oksana M; Wu, Bin; Abdulla, Arian; Segall, Jeffrey E; Verkhusha, Vladislav V

    2010-03-23

    Two-photon microscopy has advanced fluorescence imaging of cellular processes in living animals. Fluorescent proteins in the blue-green wavelength range are widely used in two-photon microscopy; however, the use of red fluorescent proteins is limited by the low power output of Ti-Sapphire lasers above 1,000 nm. To overcome this limitation we have developed two red fluorescent proteins, LSS-mKate1 and LSS-mKate2, which possess large Stokes shifts with excitation/emission maxima at 463/624 and 460/605 nm, respectively. These LSS-mKates are characterized by high pH stability, photostability, rapid chromophore maturation, and monomeric behavior. They lack absorbance in the green region, providing an additional red color to the commonly used red fluorescent proteins. Substantial overlap between the two-photon excitation spectra of the LSS-mKates and blue-green fluorophores enables multicolor imaging using a single laser. We applied this approach to a mouse xenograft model of breast cancer to intravitally study the motility and Golgi-nucleus alignment of tumor cells as a function of their distance from blood vessels. Our data indicate that within 40 mum the breast cancer cells show significant polarization towards vessels in living mice.

  4. Large-volume protein crystal growth for neutron macromolecular crystallography

    SciTech Connect

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; Garcia-Ruiz, Juan M.; Hodge, Teresa A.; Huang, Sijay

    2015-03-30

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  5. Large-volume protein crystal growth for neutron macromolecular crystallography

    DOE PAGES

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; ...

    2015-03-30

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for themore » growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.« less

  6. Protein packing: dependence on protein size, secondary structure and amino acid composition.

    PubMed

    Fleming, P J; Richards, F M

    2000-06-02

    We have used the occluded surface algorithm to estimate the packing of both buried and exposed amino acid residues in protein structures. This method works equally well for buried residues and solvent-exposed residues in contrast to the commonly used Voronoi method that works directly only on buried residues. The atomic packing of individual globular proteins may vary significantly from the average packing of a large data set of globular proteins. Here, we demonstrate that these variations in protein packing are due to a complex combination of protein size, secondary structure composition and amino acid composition. Differences in protein packing are conserved in protein families of similar structure despite significant sequence differences. This conclusion indicates that quality assessments of packing in protein structures should include a consideration of various parameters including the packing of known homologous proteins. Also, modeling of protein structures based on homologous templates should take into account the packing of the template protein structure.

  7. The richness of the globular cluster system of NGC 3923: Clues to elliptical galaxy formation

    NASA Technical Reports Server (NTRS)

    Zepf, Stephen E.; Geisler, Doug; Ashman, Keith M.

    1994-01-01

    We present new data on the globular cluster system of the elliptical galaxy NGC 3923 which show that it has the most globular clusters per unit luminosity of any noncluster elliptical yet observed, with S(sub N) = 6.4 +/- 1.4. NGC 3923 is also among the brightest ellipticals outside of a galaxy cluster for which the number of globular clusters has been determined. Our observation of a large number of clusters per unit luminosity (high S(sub N)-value) for a bright elliptical in a sparse environment is consistent with the suggestion of Djorgovski and Santiago that the number of globular clusters is a power-law function of the luminosity with an exponent greater than 1. We relate this higher specific frequency of globular clusters in more luminous galaxies to other observations which indicate that the physical conditions within elliptical galaxies at the time of their formation were dependent on galaxy mass.

  8. The Counterparts of the Luminous, Bursting X-ray Sources in Globular Clusters-LTSA98

    NASA Technical Reports Server (NTRS)

    Anderson, Scott F.

    2003-01-01

    Under the fifth year of the LTSA, we have extended our HST and Chandra work to a number of additional globular clusters. The remarkable sensitivity and positional accuracy of the Chandra observations are enabling us to maximally exploit HST for UV/optical identifications for X-ray binaries in the cores of multiple globular clusters. The dozens of lower-luminosity X-ray sources in each globular cluster deeply examined thus far have moved us firmly into the era of studies which encompass populations of close; the large range of cluster properties we are studying have, for the first tine, established a firm empirical confirmation of the (long-suspected theoretically) high importance that close binaries play in the dynamical stability and evolution of globular clusters. The LTSA support has been a cornerstone of our success over the past 5 years in studies of globular cluster X-ray sources and their counterparts.

  9. Spectroscopy of globular clusters in the outer halo of M81

    NASA Astrophysics Data System (ADS)

    Suwannajak, Chutipong; Sarajedini, Ata

    2017-01-01

    We present integrated spectroscopy of two globular clusters and two globular cluster candidates in the central region of the dynamically active M81 group of galaxies. These spectra were obtained from the OSIRIS instrument at the 10.4m Gran Telescopio Canarias (GTC). The target clusters are located in the halo between M81, M82, and NGC3077, which contains a significant amount of young stars and HI gas as a result of interactions between these galaxies. The spectra of the target clusters show spectral features of globular clusters, confirming their globular cluster nature. One of the two clusters is located 400 kpc away from M81, making it the most isolated globular cluster in the local universe. However, the origin of these clusters is still largely a mystery. We use their spectra to study their kinematics, ages, and metallicities to better understand the impact of galaxy interactions on the process of galaxy formation and evolution.

  10. Discovery of Manassantin A Protein Targets Using Large-Scale Protein Folding and Stability Measurements.

    PubMed

    Geer Wallace, M Ariel; Kwon, Do-Yeon; Weitzel, Douglas H; Lee, Chen-Ting; Stephenson, Tesia N; Chi, Jen-Tsan; Mook, Robert A; Dewhirst, Mark W; Hong, Jiyong; Fitzgerald, Michael C

    2016-08-05

    Manassantin A is a natural product that has been shown to have anticancer activity in cell-based assays, but has a largely unknown mode-of-action. Described here is the use of two different energetics-based approaches to identify protein targets of manassantin A. Using the stability of proteins from rates of oxidation technique with an isobaric mass tagging strategy (iTRAQ-SPROX) and the pulse proteolysis technique with a stable isotope labeling with amino acids in cell culture strategy (SILAC-PP), over 1000 proteins in a MDA-MB-231 cell lysate grown under hypoxic conditions were assayed for manassantin A interactions (both direct and indirect). A total of 28 protein hits were identified with manassantin A-induced thermodynamic stability changes. Two of the protein hits (filamin A and elongation factor 1α) were identified using both experimental approaches. The remaining 26 hit proteins were only assayed in either the iTRAQ-SPROX or the SILAC-PP experiment. The 28 potential protein targets of manassantin A identified here provide new experimental avenues along which to explore the molecular basis of manassantin A's mode of action. The current work also represents the first application iTRAQ-SPROX and SILAC-PP to the large-scale analysis of protein-ligand binding interactions involving a potential anticancer drug with an unknown mode-of-action.

  11. SIZES OF GALACTIC GLOBULAR CLUSTERS

    SciTech Connect

    Van den Bergh, Sidney

    2012-02-20

    A study is made of deviations from the mean power-law relationship between the Galactocentric distances and the half-light radii of Galactic globular clusters. Surprisingly, deviations from the mean R{sub h} versus R{sub gc} relationship do not appear to correlate with cluster luminosity, cluster metallicity, or horizontal-branch morphology. Differences in orbit shape are found to contribute to the scatter in the R{sub h} versus R{sub gc} relationship of Galactic globular clusters.

  12. A large solvent isotope effect on protein association thermodynamics.

    PubMed

    Eginton, Christopher; Beckett, Dorothy

    2013-09-24

    Solvent reorganization can contribute significantly to the energetics of protein-protein interactions. However, our knowledge of the magnitude of the energetic contribution is limited, in part, by a dearth of quantitative experimental measurements. The biotin repressor forms a homodimer as a prerequisite to DNA binding to repress transcription initiation. At 20 °C, the dimerization reaction, which is thermodynamically coupled to binding of a small ligand, bio-5'-AMP, is characterized by a Gibbs free energy of -7 kcal/mol. This modest net dimerization free energy reflects underlying, very large opposing enthalpic and entropic driving forces of 41 ± 3 and -48 ± 3 kcal/mol, respectively. The thermodynamics have been interpreted as indicating coupling of solvent release to dimerization. In this work, this interpretation has been investigated by measuring the effect of replacing H2O with D2O on the dimerization thermodynamics. Sedimentation equilibrium measurements performed at 20 °C reveal a solvent isotope effect of -1.5 kcal/mol on the Gibbs free energy of dimerization. Analysis of the temperature dependence of the reaction in D2O indicates enthalpic and entropic contributions of 28 and -37 kcal/mol, respectively, considerably smaller than the values measured in H2O. These large solvent isotope perturbations to the thermodynamics are consistent with a significant contribution of solvent release to the dimerization reaction.

  13. No energy equipartition in globular clusters

    NASA Astrophysics Data System (ADS)

    Trenti, Michele; van der Marel, Roeland

    2013-11-01

    It is widely believed that globular clusters evolve over many two-body relaxation times towards a state of energy equipartition, so that velocity dispersion scales with stellar mass as σ ∝ m-η with η = 0.5. We show here that this is incorrect, using a suite of direct N-body simulations with a variety of realistic initial mass functions and initial conditions. No simulated system ever reaches a state close to equipartition. Near the centre, the luminous main-sequence stars reach a maximum ηmax ≈ 0.15 ± 0.03. At large times, all radial bins convergence on an asymptotic value η∞ ≈ 0.08 ± 0.02. The development of this `partial equipartition' is strikingly similar across our simulations, despite the range of different initial conditions employed. Compact remnants tend to have higher η than main-sequence stars (but still η < 0.5), due to their steeper (evolved) mass function. The presence of an intermediate-mass black hole (IMBH) decreases η, consistent with our previous findings of a quenching of mass segregation under these conditions. All these results can be understood as a consequence of the Spitzer instability for two-component systems, extended by Vishniac to a continuous mass spectrum. Mass segregation (the tendency of heavier stars to sink towards the core) has often been studied observationally, but energy equipartition has not. Due to the advent of high-quality proper motion data sets from the Hubble Space Telescope, it is now possible to measure η for real clusters. Detailed data-model comparisons open up a new observational window on globular cluster dynamics and evolution. A first comparison of our simulations to observations of Omega Cen yields good agreement, supporting the view that globular clusters are not generally in energy equipartition. Modelling techniques that assume equipartition by construction (e.g. multi-mass Michie-King models) are approximate at best.

  14. HUBBLE SPIES GLOBULAR CLUSTER IN NEIGHBORING GALAXY

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Hubble Space Telescope has captured a view of a globular cluster called G1, a large, bright ball of light in the center of the photograph consisting of at least 300,000 old stars. G1, also known as Mayall II, orbits the Andromeda galaxy (M31), the nearest major spiral galaxy to our Milky Way. Located 130,000 light-years from Andromeda's nucleus, G1 is the brightest globular cluster in the Local Group of galaxies. The Local Group consists of about 20 nearby galaxies, including the Milky Way. The crisp image is comparable to ground-based telescope views of similar clusters orbiting the Milky Way. The Andromeda cluster, however, is nearly 100 times farther away. A glimpse into the cluster's finer details allow astronomers to see its fainter helium-burning stars whose temperatures and brightnesses show that this cluster in Andromeda and the oldest Milky Way clusters have approximately the same age. These clusters probably were formed shortly after the beginning of the universe, providing astronomers with a record of the earliest era of galaxy formation. During the next two years, astronomers will use Hubble to study about 20 more globular clusters in Andromeda. The color picture was assembled from separate images taken in visible and near-infrared wavelengths taken in July of 1994. CREDIT: Michael Rich, Kenneth Mighell, and James D. Neill (Columbia University), and Wendy Freedman (Carnegie Observatories), and NASA Image files in GIF and JPEG format and captions may be accessed on Internet via anonymous ftp from oposite.stsci.edu in /pubinfo.

  15. Large Ribosomal Protein 4 Increases Efficiency of Viral Recoding Sequences

    PubMed Central

    Green, Lisa; Houck-Loomis, Brian; Yueh, Andrew

    2012-01-01

    Expression of retroviral replication enzymes (Pol) requires a controlled translational recoding event to bypass the stop codon at the end of gag. This recoding event occurs either by direct suppression of termination via the insertion of an amino acid at the stop codon (readthrough) or by alteration of the mRNA reading frame (frameshift). Here we report the effects of a host protein, large ribosomal protein 4 (RPL4), on the efficiency of recoding. Using a dual luciferase reporter assay, we found that transfection of cells with a plasmid encoding RPL4 cDNA increases recoding efficiency in a dose-dependent manner, with a maximal enhancement of nearly twofold. Expression of RPL4 increases recoding of reporters containing retroviral readthrough and frameshift sequences, as well as the Sindbis virus leaky termination signal. RPL4-induced enhancement of recoding is cell line specific and appears to be specific to RPL4 among ribosomal proteins. Cotransfection of RPL4 cDNA with Moloney murine leukemia proviral DNA results in Gag processing defects and a reduction of viral particle formation, presumably caused by the RPL4-dependent alteration of the Gag-to-Gag-Pol ratio required for virion assembly and release. PMID:22718819

  16. APoc: large-scale identification of similar protein pockets

    PubMed Central

    Gao, Mu; Skolnick, Jeffrey

    2013-01-01

    Motivation: Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes, or ‘pockets’, on the protein’s surface. An efficient method for comparing these pockets could greatly assist the classification of ligand-binding sites, prediction of protein molecular function and design of novel drug compounds. Results: We introduce a computational method, APoc (Alignment of Pockets), for the large-scale, sequence order-independent, structural comparison of protein pockets. A scoring function, the Pocket Similarity Score (PS-score), is derived to measure the level of similarity between pockets. Statistical models are used to estimate the significance of the PS-score based on millions of comparisons of randomly related pockets. APoc is a general robust method that may be applied to pockets identified by various approaches, such as ligand-binding sites as observed in experimental complex structures, or predicted pockets identified by a pocket-detection method. Finally, we curate large benchmark datasets to evaluate the performance of APoc and present interesting examples to demonstrate the usefulness of the method. We also demonstrate that APoc has better performance than the geometric hashing-based method SiteEngine. Availability and implementation: The APoc software package including the source code is freely available at http://cssb.biology.gatech.edu/APoc. Contact: skolnick@gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23335017

  17. Measuring the bioactivity and molecular conformation of typically globular proteins with phenothiazine-derived methylene blue in solid and in solution: A comparative study using photochemistry and computational chemistry.

    PubMed

    Ding, Fei; Xie, Yong; Peng, Wei; Peng, Yu-Kui

    2016-05-01

    Methylene blue is a phenothiazine agent, that possesses a diversity of biomedical and biological therapeutic purpose, and it has also become the lead compound for the exploitation of other pharmaceuticals such as chlorpromazine and the tricyclic antidepressants. However, the U.S. Food and Drug Administration has acquired cases of detrimental effects of methylene blue toxicities such as hemolytic anemia, methemoglobinemia and phototoxicity. In this work, the molecular recognition of methylene blue by two globular proteins, hemoglobin and lysozyme was characterized by employing fluorescence, circular dichroism (CD) along with molecular modeling at the molecular scale. The recognition of methylene blue with proteins appears fluorescence quenching via static type, this phenomenon does cohere with time-resolved fluorescence lifetime decay that nonfluorescent protein-drug conjugate formation has a strength of 10(4)M(-1), and the primary noncovalent bonds, that is hydrogen bonds, π-conjugated effects and hydrophobic interactions were operated and remained adduct stable. Meantime, the results of far-UV CD and synchronous fluorescence suggest that the α-helix of hemoglobin/lysozyme decreases from 78.2%/34.7% (free) to 58.7%/23.8% (complex), this elucidation agrees well with the elaborate description of three-dimensional fluorescence showing the polypeptide chain of proteins partially destabilized upon conjugation with methylene blue. Furthermore, both extrinsic fluorescent indicator and molecular modeling clearly exhibit methylene blue is situated within the cavity constituted by α1, β2 and α2 subunits of hemoglobin, while it was located at the deep fissure on the lysozyme surface and Trp-62 and Trp-63 residues are nearby. With the aid of computational analyses and combining the wet experiments, it can evidently be found that the recognition ability of proteins for methylene blue is patterned upon the following sequence: lysozyme

  18. The binding of myristoylated N-terminal nonapeptide from neuro-specific protein CAP-23/NAP-22 to calmodulin does not induce the globular structure observed for the calmodulin-nonmyristylated peptide complex.

    PubMed Central

    Hayashi, N.; Izumi, Y.; Titani, K.; Matsushima, N.

    2000-01-01

    CAP-23/NAP-22, a neuron-specific protein kinase C substrate, is Nalpha-myristoylated and interacts with calmodulin (CaM) in the presence of Ca2+ ions. Takasaki et al. (1999, J Biol Chem 274:11848-11853) have recently found that the myristoylated N-terminal nonapeptide of CAP-23/NAP-22 (mC/N9) binds to Ca2+ -bound CaM (Ca2+/CaM). In the present study, small-angle X-ray scattering was used to investigate structural changes of Ca2+/CaM induced by its binding to mC/N9 in solution. The binding of one mC/N9 molecule induced an insignificant structural change in Ca2+/CaM. The 1:1 complex appeared to retain the extended conformation much like that of Ca2+/CaM in isolation. However, it could be seen that the binding of two mC/N9 molecules induced a drastic structural change in Ca2+/CaM, followed by a slight structural change by the binding of more than two but less than four mC/N9 molecules. Under the saturated condition (the molar ratio of 1:4), the radius of gyration (Rg) for the Ca2+/CaM-mC/N9 complex was 19.8 +/- 0.3 A. This value was significantly smaller than that of Ca2+/CaM (21.9 +/- 0.3 A), which adopted a dumbbell structure and was conversely 2-3 A larger than those of the complexes of Ca2+/CaM with the nonmyristoylated target peptides of myosin light chain kinase or CaM kinase II, which adopted a compact globular structure. The pair distance distribution function had no shoulder peak at around 40 A, which was mainly due to the dumbbell structure. These results suggest that Ca2+/CaM interacts with Nalpha-myristoylated CAP-23/NAP-22 differently than it does with other nonmyristoylated target proteins. The N-terminal amino acid sequence alignment of CAP-23/NAP-22 and other myristoylated proteins suggests that the protein myristoylation plays important roles not only in the binding of CAP-23/NAP-22 to Ca2+/CaM, but also in the protein-protein interactions related to other myristoylated proteins. PMID:11106163

  19. Secondary Globular Cluster populations

    NASA Astrophysics Data System (ADS)

    Fritze-v. Alvensleben, U.

    2004-02-01

    This study is motivated by two facts: 1. The formation of populous star cluster systems is widely observed to accompany violent star formation episodes in gas-rich galaxies as e.g. those triggered by strong interactions or merging. 2. The Globular Cluster (GC) systems of most but not all early-type galaxies show bimodal optical color distributions with fairly universal blue peaks and somewhat variable red peak colors, yet their Luminosity Functions (LFs) look like simple Gaussians with apparently universal turn-over magnitudes that are used for distance measurements and the determination of Ho. Based on a new set of evolutionary synthesis models for Simple (= single burst) Stellar Populations (SSPs) of various metallicities using the latest Padova isochrones I study the color and luminosity evolution of GC populations over the wavelength range from U through K, providing an extensive grid of models for comparison with observations. I assume the intrinsic widths of the color distributions and LFs to be constant in time at the values observed today for the Milky Way or M 31 halo GC populations. Taking the color distributions and LFs of the Milky Way or M 31 halo GC population as a reference for old metal-poor GC populations in general, I study for which combinations of age and metallicity a secondary GC population formed in some violent star formation event in the history of its parent galaxy may or may not be detected in the observed GC color distributions. I also investigate the effect of these secondary GCs on the LFs of the total GC system. Significant differences are found among the diagnostic efficiencies in various wavelength regions. In particular, we predict the NIR to be able to reveal the presence of GC subpopulations with different age - metallicity combinations that may perfectly hide within one inconspicuous optical color peak. If the entire manifold of possible age - metallicity combinations is admitted for a secondary GC population, we find several

  20. Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50.

    PubMed

    Romero Romero, M Luisa; Rabin, Avigayel; Tawfik, Dan S

    2016-12-23

    First and foremost: Margaret Dayhoff's 1966 hypothesis on the origin of proteins is now an accepted model for the emergence of large, globular, functional proteins from short, simple peptides. However, the fundamental question of how the first protein(s) emerged still stands. The tools and hypotheses pioneered by Dayhoff, and the over 65 million protein sequences and 12 000 structures known today, enable those who follow in her footsteps to address this question.

  1. Photoswitchable red fluorescent protein with a large Stokes shift.

    PubMed

    Piatkevich, Kiryl D; English, Brian P; Malashkevich, Vladimir N; Xiao, Hui; Almo, Steven C; Singer, Robert H; Verkhusha, Vladislav V

    2014-10-23

    A subclass of fluorescent proteins (FPs), large Stokes shift (LSS) FP, are characterized by increased spread between excitation and emission maxima. We report a photoswitchable variant of a red FP with an LSS, PSLSSmKate, which initially exhibits excitation and emission at 445 and 622 nm, but violet irradiation photoswitches PSLSSmKate into a common red form with excitation and emission at 573 and 621 nm. We characterize spectral, photophysical, and biochemical properties of PSLSSmKate in vitro and in mammalian cells and determine its crystal structure in the LSS form. Mass spectrometry, mutagenesis, and spectroscopy of PSLSSmKate allow us to propose molecular mechanisms for the LSS, pH dependence, and light-induced chromophore transformation. We demonstrate the applicability of PSLSSmKate to superresolution photoactivated localization microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects.

  2. Identification of the zinc-dependent endothelial cell binding protein for high molecular weight kininogen and factor XII: identity with the receptor that binds to the globular "heads" of C1q (gC1q-R).

    PubMed Central

    Joseph, K; Ghebrehiwet, B; Peerschke, E I; Reid, K B; Kaplan, A P

    1996-01-01

    High molecular weight kininogen (HK) and factor XII are known to bind to human umbilical vein endothelial cells (HUVEC) in a zinc-dependent and saturable manner indicating that HUVEC express specific binding site(s) for those proteins. However, identification and immunochemical characterization of the putative receptor site(s) has not been previously accomplished. In this report, we have identified a cell surface glycoprotein that is a likely candidate for the HK binding site on HUVECs. When solubilized HUVEC membranes were subjected to an HK-affinity column in the presence or absence of 50 microM ZnCl2 and the bound membrane proteins eluted, a single major protein peak was obtained only in the presence of zinc. SDS/PAGE analysis and silver staining of the protein peak revealed this protein to be 33 kDa and partial sequence analysis matched the NH2 terminus of gC1q-R, a membrane glycoprotein that binds to the globular "heads" of C1q. Two other minor proteins of approximately 70 kDa and 45 kDa were also obtained. Upon analysis by Western blotting, the 33-kDa band was found to react with several monoclonal antibodies (mAbs) recognizing different epitopes on gC1q-R. Ligand and dot blot analyses revealed zinc-dependent binding of biotinylated HK as well as biotinylated factor XII to the isolated 33-kDa HUVEC molecule as well as recombinant gC1q-R. In addition, binding of 125I-HK to HUVEC cells was inhibited by selected monoclonal anti-gC1q-R antibodies. C1q, however, did not inhibit 125I-HK binding to HUVEC nor did those monoclonals known to inhibit C1q binding to gC1q-R. Taken together, the data suggest that HK (and factor XII) bind to HUVECs via a 33-kDa cell surface glycoprotein that appears to be identical to gC1q-R but interact with a site on gC1q-R distinct from that which binds C1q. Images Fig. 1 Fig. 3 Fig. 4 Fig. 5 PMID:8710908

  3. EVIDENCE FOR AN ACCRETION ORIGIN FOR THE OUTER HALO GLOBULAR CLUSTER SYSTEM OF M31

    SciTech Connect

    Mackey, A. D.; Huxor, A. P.; Ferguson, A. M. N.; Irwin, M. J.; Chapman, S. C.; Tanvir, N. R.; McConnachie, A. W.; Ibata, R. A.; Lewis, G. F.

    2010-07-01

    We use a sample of newly discovered globular clusters from the Pan-Andromeda Archaeological Survey (PAndAS) in combination with previously cataloged objects to map the spatial distribution of globular clusters in the M31 halo. At projected radii beyond {approx}30 kpc, where large coherent stellar streams are readily distinguished in the field, there is a striking correlation between these features and the positions of the globular clusters. Adopting a simple Monte Carlo approach, we test the significance of this association by computing the probability that it could be due to the chance alignment of globular clusters smoothly distributed in the M31 halo. We find that the likelihood of this possibility is low, below 1%, and conclude that the observed spatial coincidence between globular clusters and multiple tidal debris streams in the outer halo of M31 reflects a genuine physical association. Our results imply that the majority of the remote globular cluster system of M31 has been assembled as a consequence of the accretion of cluster-bearing satellite galaxies. This constitutes the most direct evidence to date that the outer halo globular cluster populations in some galaxies are largely accreted.

  4. Denatured globular protein and bile salt-coated nanoparticles for poorly water-soluble drugs: Penetration across the intestinal epithelial barrier into the circulation system and enhanced oral bioavailability.

    PubMed

    He, Wei; Yang, Ke; Fan, Lifang; Lv, Yaqi; Jin, Zhu; Zhu, Shumin; Qin, Chao; Wang, Yiao; Yin, Lifang

    2015-11-10

    Oral drug delivery is the most preferred route for patients; however, the low solubility of drugs and the resultant poor absorption compromise the benefits of oral administration. On the other hand, for years, the overwhelmingly accepted mechanism for enhanced oral absorption using lipid nanocarriers was based on the process of lipid digestion and drug solubilization in the small intestine. Few reports indicated that other bypass pathways are involved in drug absorption in the gastrointestinal tract (GIT) for oral delivery of nanocarriers. Herein, we report a new nanoemulsion system with a denatured globular protein with a diameter of 30 nm, soybean protein isolates (SPI), and bile salt as emulsifiers, aiming to enhance the absorption of insoluble drugs and explore other pathways for absorption. A BCS class II drug, fenofibrate (FB), was used as the model drug. The SPI and bile salt-coated Ns with a diameter of approximately 150 nm were prepared via a high-pressure homogenizing procedure. Interestingly, the present Ns could be converted to solid dosage form using fluid-bed coating technology, maintaining a nanoscale size. Most importantly, in a model of in situ rat intestinal perfusion, Ns could penetrate across the intestinal epithelial barrier into the systemic circulation and then obtain biodistribution into other tissues. In addition, Ns significantly improved FB oral absorption, exhibited as a greater than 2- and 2.5-fold increase in Cmax and AUC0-t, respectively, compared to the suspension formulation. Overall, the present Ns are promising nanocarriers for the oral delivery of insoluble drugs, and the penetration of intact Ns across the GIT barrier into systemic circulation may be a new strategy for improved drug absorption with the use of nanocarriers.

  5. Recent excitements in protein NMR: Large proteins and biologically relevant dynamics.

    PubMed

    Chiliveri, Sai Chaitanya; Deshmukh, Mandar V

    2016-12-01

    The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecular NMR spectroscopists to overcome the size limitation barrier (approx. 20 kDa) in de novo structure determination of proteins. The utility of these techniques was immediately demonstrated on large proteins and protein complexes (e.g. GroELGroES, ClpP protease, Hsp90-p53, 20S proteasome, etc.). Further, recent methodological developments such as Residual Dipolar Couplings and Paramagnetic Relaxation Enhancement allowed accurate measurement of long-range structural restraints. Additionally, Carr-Purcell-Meiboom-Gill (CPMG), rotating frame relaxation experiments (R1(rho)) and saturation transfer experiments (CEST and DEST) created never-before accessibility to the (mu)s-ms timescale dynamic parameters that led to the deeper understanding of biological processes. Meanwhile, the excitement in the field continued with a series of developments in the fast data acquisition methods allowing rapid structural studies on less stable proteins. This review aims to discuss important developments in the field of biomolecular NMR spectroscopy in the recent past, i.e., in the post TROSY era. These developments not only gave access to the structural studies of large protein assemblies, but also revolutionized tools in the arsenal of today's biomolecular NMR and point to a bright future of biomolecular NMR spectroscopy.

  6. Photooxidation of Tryptophan and Tyrosine Residues in Human Serum Albumin Sensitized by Pterin: A Model for Globular Protein Photodamage in Skin.

    PubMed

    Reid, Lara O; Roman, Ernesto A; Thomas, Andrés H; Dántola, M Laura

    2016-08-30

    Human serum albumin (HSA) is the most abundant protein in the circulatory system. Oxidized albumin was identified in the skin of patients suffering from vitiligo, a depigmentation disorder in which the protection against ultraviolet (UV) radiation fails because of the lack of melanin. Oxidized pterins, efficient photosensitizers under UV-A irradiation, accumulate in the skin affected by vitiligo. In this work, we have investigated the ability of pterin (Ptr), the parent compound of oxidized pterins, to induce structural and chemical changes in HSA under UV-A irradiation. Our results showed that Ptr is able to photoinduce oxidation of the protein in at least two amino acid residues: tryptophan (Trp) and tyrosine (Tyr). HSA undergoes oligomerization, yielding protein structures whose molecular weight increases with irradiation time. The protein cross-linking, due to the formation of dimers of Tyr, does not significantly affect the secondary and tertiary structures of HSA. Trp is consumed in the photosensitized process, and N-formylkynurenine was identified as one of its oxidation products. The photosensitization of HSA takes place via a purely dynamic process, which involves the triplet excited state of Ptr. The results presented in this work suggest that protein photodamage mediated by endogenous photosensitizers can significantly contribute to the harmful effects of UV-A radiation on the human skin.

  7. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

    PubMed Central

    Delaforge, Elise; Milles, Sigrid; Huang, Jie-rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J.; Blackledge, Martin

    2016-01-01

    Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales. PMID:27679800

  8. DARK MATTER HALOS IN GALAXIES AND GLOBULAR CLUSTER POPULATIONS

    SciTech Connect

    Hudson, Michael J.; Harris, Gretchen L.; Harris, William E.

    2014-05-20

    We combine a new, comprehensive database for globular cluster populations in all types of galaxies with a new calibration of galaxy halo masses based entirely on weak lensing. Correlating these two sets of data, we find that the mass ratio η ≡ M {sub GCS}/M {sub h} (total mass in globular clusters, divided by halo mass) is essentially constant at (η) ∼ 4 × 10{sup –5}, strongly confirming earlier suggestions in the literature. Globular clusters are the only known stellar population that formed in essentially direct proportion to host galaxy halo mass. The intrinsic scatter in η appears to be at most 0.2 dex; we argue that some of this scatter is due to differing degrees of tidal stripping of the globular cluster systems between central and satellite galaxies. We suggest that this correlation can be understood if most globular clusters form at very early stages in galaxy evolution, largely avoiding the feedback processes that inhibited the bulk of field-star formation in their host galaxies. The actual mean value of η also suggests that about one-fourth of the initial gas mass present in protogalaxies collected into giant molecular clouds large enough to form massive, dense star clusters. Finally, our calibration of (η) indicates that the halo masses of the Milky Way and M31 are (1.2 ± 0.5) × 10{sup 12} M {sub ☉} and (3.9 ± 1.8) × 10{sup 12} M {sub ☉}, respectively.

  9. Temporal Variant Frontotemporal Dementia is Associated with Globular Glial Tauopathy.

    PubMed

    Clark, Camilla N; Lashley, Tammaryn; Mahoney, Colin J; Warren, Jason D; Revesz, Tamas; Rohrer, Jonathan D

    2015-06-01

    Frontotemporal dementia (FTD) is a clinically and pathologically heterogeneous neurodegenerative disorder associated with atrophy of the frontal and temporal lobes. Most patients with focal temporal lobe atrophy present with either the semantic dementia subtype of FTD or the behavioral variant subtype. For patients with temporal variant FTD, the most common cause found on post-mortem examination has been a TDP-43 (transactive response DNA-binding protein 43 kDa) proteinopathy, but tauopathies have also been described, including Pick's disease and mutations in the microtubule-associated protein tau (MAPT) gene. We report the clinical and imaging features of 2 patients with temporal variant FTD associated with a rare frontotemporal lobar degeneration pathology known as globular glial tauopathy. The pathologic diagnosis of globular glial tauopathy should be considered in patients with temporal variant FTD, particularly those who have atypical semantic dementia or an atypical parkinsonian syndrome in association with the right temporal variant.

  10. Adsorption of globular proteins on locally planar surfaces. II. Models for the effect of multiple adsorbate conformations on adsorption equilibria and kinetics.

    PubMed Central

    Minton, A P

    1999-01-01

    Equilibrium and kinetic models for nonspecific adsorption of proteins to planar surfaces are presented. These models allow for the possibility of multiple interconvertible surface conformations of adsorbed protein. Steric repulsion resulting in area exclusion by adsorbed molecules is taken into account by treating the adsorbate as a thermodynamically nonideal two-dimensional fluid. In the equilibrium model, the possibility of attractive interactions between adsorbed molecules is taken into account in a limited fashion by permitting one of the adsorbed species to self-associate. Calculated equilibrium adsorption isotherms exhibit apparent high-affinity and low-affinity binding regions, corresponding respectively to adsorption of ligand at low fractional area occupancy in an energetically favorable side-on conformation and conversion at higher fractional area occupancy of the side-on conformation to an entropically favored end-on conformation. Adsorbate self-association may lead to considerable steepening of the adsorption isotherm, compensating to a variable extent for the broadening effect of steric repulsion. Kinetic calculations suggest that in the absence of attractive interactions between adsorbate molecules, the process of adsorption may be highly "stretched" along the time axis, rendering the attainment of adsorption equilibrium in the context of conventional experiments problematic. PMID:9876132

  11. Globular body production, their anatomy, DNase gel analysis and NDP kinase activity in root tips of Poncirus trifoliata L.

    PubMed

    Tzatzani, Thiresia-Teresa; Dimassi-Theriou, Kortessa; Yupsanis, Traianos; Bosabalidis, Artemios; Therios, Ioannis; Sarropoulou, Virginia

    2013-10-01

    Green globular bodies were developed from Poncirus trifoliata L. root tip explants as a response to addition in the substrate of different growth regulators. From the globular bodies, shoots initiated and grew. Median section of the globular bodies reveals that they are composed of parenchyma cells and originate from the pericycle. The activity of DNases during shoot formation from globular bodies was influenced by the type and concentration of plant growth regulators that were added in the nutrient substrate. Peptide bands formation was also influenced by the increase of BA concentration. Consequently, BA, NAA and IAA combination influenced 5'-triphosphonucleosides (NTPs) appearance and activity in the presence of metal. Peptide bands resulted from the electrophoretic analysis of endogenous protein phosphorylation, proved to be catalytic subunits of NDP kinases, as they all phosphorylate diphosphonucleosides. The enzymes DNases and NDP kinases could be used as a scientific tool for the study of shoot formation from P. trifoliata L. green globular bodies.

  12. Lack of Energy Equipartition in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Trenti, Michele

    2013-05-01

    Abstract (2,250 Maximum Characters): It is widely believed that globular clusters evolve over many two-body relaxation times toward a state of energy equipartition, so that velocity dispersion scales with stellar mass as σ∝m^{-η} with η=0.5. I will show instead that this is incorrect, using a suite of direct N-body simulations with a variety of realistic initial mass functions and initial conditions. No simulated system ever reaches a state close to equipartition. Near the center, the luminous main-sequence stars reach a maximum η_{max 0.15±0.03. At large times, all radial bins convergence on an asymptotic value η_{∞ 0.08±0.02. The development of this ``partial equipartition'' is strikingly similar across simulations, despite the range of different initial conditions employed. Compact remnants tend to have higher η than main-sequence stars (but still η< 0.5), due to their steeper (evolved) mass function. The presence of an intermediate-mass black hole (IMBH) decreases η, consistent with our previous findings of a quenching of mass segregation under these conditions. All these results can be understood as a consequence of the Spitzer instability for two-component systems, extended by Vishniac to a continuous mass spectrum. Mass segregation (the tendency of heavier stars to sink toward the core) has often been studied observationally, but energy equipartition has not. Due to the advent of high-quality proper motion datasets from the Hubble Space Telescope, it is now possible to measure η for real clusters. Detailed data-model comparisons open up a new observational window on globular cluster dynamics, structure, evolution, initial conditions, and possible IMBHs. A first comparison of my simulations to observations of Omega Cen yields good agreement, supporting the view that globular clusters are not generally in energy equipartition. Modeling techniques that assume equipartition by construction (e.g., multi-mass Michie-King models) are thus approximate

  13. Photometric binary stars in Praesepe and the search for globular cluster binaries

    NASA Technical Reports Server (NTRS)

    Bolte, Michael

    1991-01-01

    A radial velocity study of the stars which are located on a second sequence above the single-star zero-age main sequence at a given color in the color-magnitude diagram of the open cluster Praesepe, (NGC 2632) shows that 10, and possibly 11, of 17 are binary systems. Of the binary systems, five have full amplitudes for their velocity variations that are greater than 50 km/s. To the extent that they can be applied to globular clusters, these results suggests that (1) observations of 'second-sequence' stars in globular clusters would be an efficient way of finding main-sequence binary systems in globulars, and (2) current instrumentation on large telescopes is sufficient for establishing unambiguously the existence of main-sequence binary systems in nearby globular clusters.

  14. Globular cluster clustering around ultra compact dwarf galaxies in the halo of NGC 1399

    NASA Astrophysics Data System (ADS)

    Voggel, Karina; Hilker, Michael; Richtler, Tom

    2016-08-01

    We tested the spatial distribution of UCDs and GCs in the halo of NGC 1399 in the Fornax cluster. In particular we tried to find out if globular clusters are more abundant in the vicinity of UCDs than what is expected from their global distribution. A local overabundance of globular clusters was found around UCDs on a scale of 1 kpc compared to what is expected from the large scale distribution of globulars in the host galaxy. This effect is stronger for the metal-poor blue GCs and weaker for the red GCs. An explanation for these clustered globulars is either that they are the remains of a GC system of an ancestor dwarf galaxy before it was stripped to its nucleus, which appears as UCD today. Alternatively these clustered GCs could have been originally part of a super star cluster complex.

  15. Development of the Dynamic Globularization Prediction Model for Ti-17 Titanium Alloy Using Finite Element Method

    NASA Astrophysics Data System (ADS)

    Jia, Zhiqiang; Zeng, Weidong; Xu, Jianwei; Zhou, Jianhua; Wang, Xiaoying

    2015-04-01

    In this work, a finite element method (FEM) model for predicting dynamic globularization of Ti-17 titanium alloy is established. For obtaining the microstructure evolution during dynamic globularization under varying processing parameters, isothermal hot compression tests and quantitative metallographic analysis were conducted on Ti-17 titanium alloy with initial lamellar microstructure. The prediction model, which quantitatively described the non-linear relationship between the dynamic globularization fraction and the deformation strain, temperature, and strain rate, was developed on the basis of the Avrami equation. Then the developed model was incorporated into DEFORM software as a user subroutine. Finally, the large-sized step-shaped workpiece was isothermally forged and corresponding FEM simulation was conducted to verify the reliability and accuracy of the integrated FEM model. The reasonable coincidence of the predicted results with experimental ones indicated that the established FEM model provides an easy and a practical method to predict dynamic globularization for Ti-17 titanium alloy with complex shape.

  16. Radial velocities of remote globular clusters - stalking the missing mass

    SciTech Connect

    Peterson, R.C.

    1985-10-01

    Measurements good to 25 km/s are presented of radial velocities of five remote galactic globular clusters, based on aperture-plate spectra of individual stars at 3.0 A resolution. Velocities with respect to the galactic rest-frame of two individual systems, Eridanus and Palomar 14, are large enough to suggest a total mass for the Galaxy of 1 trillion solar masses. A similar mass is inferred from the average of the galactocentric distance times velocity squared. 36 references.

  17. Predictions of a population of cataclysmic variables in globular clusters

    NASA Technical Reports Server (NTRS)

    Di Stefano, R.; Rappaport, S.

    1994-01-01

    We have studied the number of cataclysmic variables (CVs) that should be active in globular clusters during the present epoch as a result of binary formation via two-body tidal capture. We predict the orbital period and luminosity distributions of CVs in globular clusters. The results arebased on Monte Carlo simulations combined with evolution calculations appropriate to each system formed during the lifetime of two specific globular clusters, omega Cen and 47 Tuc. From our study of these two clusters, which represent the range of core densities and states of mass segregation that are likely to be interesting, we extrapolate our results to the Galactic globlular cluster system. Although there is at present little direct observational evidence of CVs in globular clusters, we find that there should be a large number of active systems. We predict that there should be more than approximately 100 CVs in both 47 Tuc and omega Cen and several thousand in the Galactic globular cluster system. These numbers are based on two-body processes alone and represent a lower bound on the number of systems that may have been formed as a result of stellar interaction within globular clusters. The relation between these calculations and the paucity of optically detected CVs in globular clusters is discussed. Should future observations fail to find convincing evidence of a substantial population of cluster CVs, then the two-body tidal capture scenario is likely to be seriously constrained. Of the CVs we espect in 47 Tuc and omega Cen, approximately 45 and 20, respectively, should have accretion luminosities above 10(exp 33) ergs/s. If one utilizes a relation for converting accretion luminosity to hard X-ray luminosity that is based on observations of Galactic plane CVs, even these sources will not exhibit X-ray luminosities above 10(exp 33) ergs/s. While we cannot account directly for the most luminous subset of the low-luminosity globular cluster X-ray sources without assuming an

  18. Oligomeric viral proteins: small in size, large in presence

    PubMed Central

    Jayaraman, Bhargavi; Smith, Amber M.; Fernandes, Jason D.; Frankel, Alan D.

    2016-01-01

    Viruses are obligate parasites that rely heavily on host cellular processes for replication. The small number of proteins typically encoded by a virus is faced with selection pressures that lead to the evolution of distinctive structural properties, allowing each protein to maintain its function under constraints such as small genome size, high mutation rate, and rapidly changing fitness conditions. One common strategy for this evolution is to utilize small building blocks to generate protein oligomers that assemble in multiple ways, thereby diversifying protein function and regulation. In this review, we discuss specific cases that illustrate how oligomerization is used to generate a single defined functional state, to modulate activity via different oligomeric states, or to generate multiple functional forms via different oligomeric states. PMID:27685368

  19. Hot stars in globular clusters.

    NASA Astrophysics Data System (ADS)

    Moehler, S.

    Globular clusters are ideal laboratories to study the evolution of low-mass stars. In this review, I shall concentrate on two types of hot stars observed in globular clusters: horizontal branch stars and UV bright stars. The third type, the white dwarfs, are covered by Bono in this volume. While the morphology of the horizontal branch correlates strongly with metallicity, it has been known for a long time that one parameter is not sufficient to describe the diversity of observed horizontal branch morphologies. A veritable zoo of candidates for this elusive ``2{nd} parameter'' has been suggested over the past decades, and the most prominent ones will be briefly discussed here. Adding to the complications, diffusion is active in the atmospheres of hot horizontal branch stars, which makes their analysis much more diffcult. The latest twist along the horizontal branch was added by the recent discovery of an extension to hotter temperatures and fainter magnitudes, the so-called ``blue hook''. The evolutionary origin of these stars is still under debate. I shall also give a brief overview of our current knowledge about hot UV bright stars and use them to illustrate the adverse effects of selection bias.

  20. The ultraviolet spectra of M31 globular clusters

    NASA Technical Reports Server (NTRS)

    Cowley, A. P.; Burstein, D.

    1988-01-01

    Ultraviolet spectra of 11 of the brightest globular clusters in M31 show that some exhibit residual flux below 3000 A, greater than that expected from the bright, evolved stars in the cluster. There seems to be no apparent correlation of the strength of this ultraviolet flux with parameters such as metallicity, U-B color, visual magnitude, X-ray emission, or location within the parent galaxy. However, comparison of the ultraviolet colors of the M31 globular clusters with those in the Galaxy and in the Large Magellanic Cloud suggests that the M31 clusters may contain a high percentage of blue horizontal-branch stars or that some clusters could be as young as about 2 x 10 to the 9th yr.

  1. Galactic bulge X-ray burst sources from disrupted globular clusters?

    NASA Technical Reports Server (NTRS)

    Grindlay, J. E.; Hertz, P.

    1985-01-01

    The origin of the bright galactic bulge X-ray sources, or GX sources, is unclear despite intensive study for the past 15 years. It is suggested that the fact that many (or most) of the GX sources are X-ray burst sources (GXRBS) and are otherwise apparently identical to the luminous X-ray sources found in globular cluster cores implies that they too may have a globular cluster origin. The possibility that the compact X-ray binaries found in globulars are ejected is constrained by observations of CVs in and out of clusters. The GXRBS are instead hypothesized to have been formed by capture processes in globular clusters which have now largely been disrupted by repeated tidal stripping and shocking in the galactic plane. A statistical analysis of the 12 GXRBS which have precise positions from Einstein and/or optical (or radio) observations indicate that it is probably significant that a bright, of less than about 19, G or K star is found within the error circle (3 arcmin radius) in four cases. These may be surviving giants in a disrupted globular cluster core. Implications for globular cluster evolution and the GXRBS themselves are discussed.

  2. Characterization of the weak calcium binding of trimeric globular adiponectin.

    PubMed

    Yu, Dongmei; Zhang, Chao; Wang, Han; Qin, Peiwu

    2013-06-01

    Adiponectin is secreted from adipose tissue and functions as a protein hormone in regulating glucose metabolism and fatty acid catabolism. Adiponectin plays an important role as a novel risk factor and potential diagnostic and prognostic biomarker in cancer. Crystal structures of globular adiponectin have been resolved with three calcium-binding sites on the top of its central tunnel. However, the calcium-binding property of adiponectin remains elusive. Mouse globular adiponectin was cloned into pET11a and expressed in Escherichia coli. The folding of adiponectin was indicated by the spread of resonances in HSQC spectrum. Luminescence resonance energy transfer was used to obtain the binding constant (K(d)) of Tb(3+) and the inhibitor constant (K(i)) of Ca(2+) for globular adiponectin. The obtained calcium-binding affinity to adiponectin is relatively low (~2 mM), which indicates that the high concentration of adiponectin in circulating system may function as calcium storage bank and buffer the free calcium concentration.

  3. Kinematics of the Globular Cluster System of the Sombrero Galaxy

    NASA Astrophysics Data System (ADS)

    Windschitl, Jessica L.; Rhode, K. L.; Bridges, T. J.; Zepf, S. E.; Gebhardt, K.; Freeman, K. C.

    2013-06-01

    Using spectra from the Hydra spectrograph on the 3.5m WIYN telescope and from the AAOmega spectrograph on the 3.9m Anglo-Australian Telescope, we have measured heliocentric radial velocities for >50 globular clusters in the Sombrero Galaxy (M104). We combine these new measurements with those from previous studies to construct and analyze a total sample of >360 globular cluster velocities in M104. We use the line-of-sight velocity dispersion to determine the mass and mass-to-light ratio profiles for the galaxy using a spherical, isotropic Jeans mass model. In addition to the increased sample size, our data provide a significant expansion in radial coverage compared to previous spectroscopic studies. This allows us to reliably compute the mass profile of M104 out to ~43 kpc, nearly 14 kpc farther into the halo than previous work. We find that the mass-to-light ratio profile increases from the center to a value of ~20 at 43 kpc. We also look for the presence of rotation in the globular cluster system as a whole and within the red and blue subpopulations. Despite the large number of clusters and better radial sampling, we do not find strong evidence of rotation.

  4. A SURVEY FOR PLANETARY NEBULAE IN M31 GLOBULAR CLUSTERS

    SciTech Connect

    Jacoby, George H.; De Marco, Orsola; Lee, Myung Gyoon; Herrmann, Kimberly A.; Hwang, Ho Seong; Davies, James E.; Kaplan, Evan E-mail: rbc@astro.psu.edu E-mail: mglee@astrog.snu.ac.kr E-mail: hhwang@cfa.harvard.edu E-mail: evanskaplan@gmail.com

    2013-05-20

    We report the results of an [O III] {lambda}5007 spectroscopic survey for planetary nebulae (PNe) located within the star clusters of M31. By examining R {approx} 5000 spectra taken with the WIYN+Hydra spectrograph, we identify 3 PN candidates in a sample of 274 likely globular clusters, 2 candidates in objects which may be globular clusters, and 5 candidates in a set of 85 younger systems. The possible PNe are all faint, between {approx}2.5 and {approx}6.8 mag down the PN luminosity function, and, partly as a consequence of our selection criteria, have high excitation, with [O III] {lambda}5007 to H{beta} ratios ranging from 2 to {approx}> 12. We discuss the individual candidates, their likelihood of cluster membership, and the possibility that they were formed via binary interactions within the clusters. Our data are consistent with the suggestion that PN formation within globular clusters correlates with binary encounter frequency, though, due to the small numbers and large uncertainties in the candidate list, this study does not provide sufficient evidence to confirm the hypothesis.

  5. Interdependence of the rad50 hook and globular domain functions.

    PubMed

    Hohl, Marcel; Kochańczyk, Tomasz; Tous, Cristina; Aguilera, Andrés; Krężel, Artur; Petrini, John H J

    2015-02-05

    Rad50 contains a conserved Zn(2+) coordination domain (the Rad50 hook) that functions as a homodimerization interface. Hook ablation phenocopies Rad50 deficiency in all respects. Here, we focused on rad50 mutations flanking the Zn(2+)-coordinating hook cysteines. These mutants impaired hook-mediated dimerization, but recombination between sister chromatids was largely unaffected. This may reflect that cohesin-mediated sister chromatid interactions are sufficient for double-strand break repair. However, Mre11 complex functions specified by the globular domain, including Tel1 (ATM) activation, nonhomologous end joining, and DNA double-strand break end resection were affected, suggesting that dimerization exerts a broad influence on Mre11 complex function. These phenotypes were suppressed by mutations within the coiled-coil and globular ATPase domains, suggesting a model in which conformational changes in the hook and globular domains are transmitted via the extended coils of Rad50. We propose that transmission of spatial information in this manner underlies the regulation of Mre11 complex functions.

  6. What determines the stellar mass functions in globular clusters?

    NASA Technical Reports Server (NTRS)

    Djorgovski, S.; Piotto, Giampaolo; Capaccioli, Massimo

    1993-01-01

    We analyze the dependence of stellar mass function slopes for a sample of 17 globular clusters on a variety of cluster parameters. The principal novelty of our approach is the use of appropriate multivariate statistical methods to disentangle the complex situation which is present in this problem: the slopes depend simultaneously on more than one variable, and many cluster parameters are mutually correlated. We find that the mass function slopes in the range M/M(solar) = 0.5-0.8 are largely determined by the position in the Galaxy and to a lesser extent by the cluster metallicity. Clusters closer to the Galactic center or plane have shallower mass function slopes. At a given distance to the Galactic center, clusters closer to the Galactic plane have shallower mass function slopes. At a given R(GC) and/or Z(GP), more metal-rich clusters have shallower mass function slopes. Thus, the monovariate correlations with the position or metallicity are both correct, but only partial, and in terms of slopes, biased descriptions of the situation. We present trivariate least-squares solutions where the mass function slopes can be predicted within the measurement accuracy. This relation can serve as a powerful observational constraint for theories of globular cluster formation and evolution, and it is one of the tightest correlations between globular cluster properties now known.

  7. Interdependence of the Rad50 hook and globular domain functions

    PubMed Central

    Hohl, Marcel; Kochańczyk, Tomasz; Tous, Cristina; Aguilera, Andrés; Krężel, Artur; Petrini, John H J

    2015-01-01

    SUMMARY Rad50 contains a conserved Zn2+ coordination domain (the Rad50 hook) that functions as a homodimerization interface. Hook ablation phenocopies Rad50 deficiency in all respects. Here we focused on rad50 mutations flanking the Zn2+-coordinating hook cysteines. These mutants impaired hook-mediated dimerization, but recombination between sister chromatids was largely unaffected. This may reflect that cohesin-mediated sister chromatid interactions are sufficient for double strand break repair. However, Mre11 complex functions specified by the globular domain, including Tel1 (ATM) activation, nonhomologous end-joining, and DNA double strand break end resection were affected, suggesting that dimerization exerts a broad influence on Mre11 complex function. These phenotypes were suppressed by mutations within the coiled coil and globular ATPase domain, suggesting a model in which conformational changes in the hook and globular domains are transmitted via the extended coils of Rad50. We propose that transmission of spatial information in this manner underlies the regulation of Mre11 complex functions. PMID:25601756

  8. Modeling the Blue Stragglers in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Chatterjee, Sourav

    2012-10-01

    Blue stragglers {BS} have been extensively observed in Galactic globular clusters {GGC}. primarily with HST. Many theoretical studies have identified BS formation channels and it is understood that dynamics in GCs modifies formation and distribution of the BSs. Despite the wealth of observational data, comprehensive theoretical models including all relevant physical processes in dynamically evolving GCs do not exist. Our dynamical cluster modeling code, developed over the past decade, includes all relevant physical processes in a GC including two-body relaxation, strong scattering, physical collisions, and stellar-evolution {single and binary}. We can model GCs with realistic N and provide star-by-star models for GCs directly comparable with the observed data. This proposed study will create realistic GC models with initial conditions from a grid spanning a large range in the multidimensional parameter space including cluster mass, binary fraction, concentration, and Galactic position. Our numerical models combined with observational constraints from existing HST data will for the first time provide explanations for the observed trends in the BS populations in GGCs, the dominant formation channel for these BSs, typical dynamical ages of the BSs, and find detailed dynamical histories of the BSs in GGCs. These models will yield valuable insight on the correlations between the BS properties and a number of cluster dynamical properties {central density, binary fraction, and binary orbital properties} which will potentially help constrain a GC's past evolutionary history. As a bonus a large set of realistic theoretical GC models will be constructed.

  9. CENTRAL ROTATIONS OF MILKY WAY GLOBULAR CLUSTERS

    SciTech Connect

    Fabricius, Maximilian H.; Rukdee, Surangkhana; Saglia, Roberto P.; Bender, Ralf; Hopp, Ulrich; Thomas, Jens; Williams, Michael J.; Noyola, Eva; Opitsch, Michael

    2014-06-01

    Most Milky Way globular clusters (GCs) exhibit measurable flattening, even if on a very low level. Both cluster rotation and tidal fields are thought to cause this flattening. Nevertheless, rotation has only been confirmed in a handful of GCs, based mostly on individual radial velocities at large radii. We are conducting a survey of the central kinematics of Galactic GCs using the new Integral Field Unit instrument VIRUS-W. We detect rotation in all 11 GCs that we have observed so far, rendering it likely that a large majority of the Milky Way GCs rotate. We use published catalogs of GCs to derive central ellipticities and position angles. We show that in all cases where the central ellipticity permits an accurate measurement of the position angle, those angles are in excellent agreement with the kinematic position angles that we derive from the VIRUS-W velocity fields. We find an unexpected tight correlation between central rotation and outer ellipticity, indicating that rotation drives flattening for the objects in our sample. We also find a tight correlation between central rotation and published values for the central velocity dispersion, most likely due to rotation impacting the old dispersion measurements.

  10. Central Rotations of Milky Way Globular Clusters

    NASA Astrophysics Data System (ADS)

    Fabricius, Maximilian H.; Noyola, Eva; Rukdee, Surangkhana; Saglia, Roberto P.; Bender, Ralf; Hopp, Ulrich; Thomas, Jens; Opitsch, Michael; Williams, Michael J.

    2014-06-01

    Most Milky Way globular clusters (GCs) exhibit measurable flattening, even if on a very low level. Both cluster rotation and tidal fields are thought to cause this flattening. Nevertheless, rotation has only been confirmed in a handful of GCs, based mostly on individual radial velocities at large radii. We are conducting a survey of the central kinematics of Galactic GCs using the new Integral Field Unit instrument VIRUS-W. We detect rotation in all 11 GCs that we have observed so far, rendering it likely that a large majority of the Milky Way GCs rotate. We use published catalogs of GCs to derive central ellipticities and position angles. We show that in all cases where the central ellipticity permits an accurate measurement of the position angle, those angles are in excellent agreement with the kinematic position angles that we derive from the VIRUS-W velocity fields. We find an unexpected tight correlation between central rotation and outer ellipticity, indicating that rotation drives flattening for the objects in our sample. We also find a tight correlation between central rotation and published values for the central velocity dispersion, most likely due to rotation impacting the old dispersion measurements. This Letter includes data taken at The McDonald Observatory of The University of Texas at Austin.

  11. Search for Carbon-Rich Asymptotic Giant Branch Stars in Milky Way Globular Clusters

    NASA Astrophysics Data System (ADS)

    Indahl, Briana; Pessev, P.

    2014-01-01

    From our current understanding of stellar evolution, it would not be expected to find carbon rich asymptotic giant branch (AGB) stars in Milky Way globular clusters. Due to the low metallicity of the population II stars making up the globular clusters and their age, stars large enough to fuse carbon should have already evolved off of the asymptotic giant branch. Recently, however, there have been serendipitous discoveries of these types of stars. Matsunaga et al. (2006) discovered a Mira variable in the globular cluster Lynga 7. It was later confirmed by Feast et al. (2012) that the star is a member of the cluster and must be a product of a stellar merger. In the same year, Sharina et al. (2012) discovered a carbon star in the low metallicity globular cluster NGC6426 and reports it to be a CH star. Five more of these types of stars have been made as serendipitous discoveries and have been reported by Harding (1962), Dickens (1972), Cote et al. (1997), and Van Loon (2007). The abundance of these types of carbon stars in Milky Way globular clusters has been unknown because the discovery of these types of objects has only ever been a serendipitous discovery. These stars could have been easily overlooked in the past as they are outside the typical parameter space of galactic globular clusters. Also advances in near-infrared instruments and observing techniques have made it possible to detect the fainter carbon stars in binary systems. Having an understanding of the abundances of carbon stars in galactic globular clusters will aid in the modeling of globular cluster and galaxy formation leading to a better understanding of these processes. To get an understanding of the abundances of these stars we conducted the first comprehensive search for AGB carbon stars into all Milky Way globular clusters listed in the Harris Catalog (expect for Pyxis). I have found 128 carbon star candidates using methods of comparing color magnitude diagrams of the clusters with the carbon

  12. A Simple and Effective Protein Folding Activity Suitable for Large Lectures

    ERIC Educational Resources Information Center

    White, Brian

    2006-01-01

    This article describes a simple and inexpensive hands-on simulation of protein folding suitable for use in large lecture classes. This activity uses a minimum of parts, tools, and skill to simulate some of the fundamental principles of protein folding. The major concepts targeted are that proteins begin as linear polypeptides and fold to…

  13. UV-bright stars in globular clusters

    NASA Technical Reports Server (NTRS)

    Landsman, Wayne B.

    1994-01-01

    This paper highlights globular cluster studies with Ultraviolet Imaging Telescope (UIT) in three areas: the discrepancy between observed ultraviolet HB magnitudes and predictions of theoretical HB models; the discovery of two hot subdwarfs in NGC 1851, a globular not previously known to contain such stars; and spectroscopic follow up of newly identified UV-bright stars in M79 and w Cen. I also present results of a recent observation of NGC 6397 with the Voyager ultraviolet spectrometer.

  14. Contribution of globular clusters to halos

    NASA Astrophysics Data System (ADS)

    Bragaglia, Angela

    2017-03-01

    The contribution of massive star clusters to their hosting halo dramatically depends on their formation mechanism and their early evolution. Massive globular clusters in the Milky Way (and in other galaxies) have been shown to display peculiar chemical patterns (light-elements correlations and anti-correlations) indicative of a complex star formation, confirmed by photometric evidence (spread or split sequences). I use these chemical signatures to try to understand what is the fraction of halo stars originally born in globular clusters.

  15. Globular clusters in the far-ultraviolet: evidence for He-enriched second populations in extragalactic globular clusters?

    NASA Astrophysics Data System (ADS)

    Peacock, Mark B.; Zepf, Stephen E.; Kundu, Arunav; Chael, Julia

    2017-01-01

    We investigate the integrated far-ultraviolet (FUV) emission from globular clusters. We present new FUV photometry of M87's clusters based on archival Hubble Space Telescope (HST) Wide Field Planetary Camera 2 F170W observations. We use these data to test the reliability of published photometry based on HST space telescope imaging spectrograph FUV-MAMA observations, which are now known to suffer from significant red-leak. We generally confirm these previous FUV detections, but suggest they may be somewhat fainter. We compare the FUV emission from bright (MV < -9.0) clusters in the Milky Way, M31, M81 and M87 to each other and to the predictions from stellar populations models. Metal-rich globular clusters show a large spread in FUV - V, with some clusters in M31, M81 and M87 being much bluer than standard predictions. This requires that some metal-rich clusters host a significant population of blue/extreme horizontal branch (HB) stars. These hot HB stars are not traditionally expected in metal-rich environments, but are a natural consequence of multiple populations in clusters - since the enriched population is observed to be He enhanced and will therefore produce bluer HB stars, even at high metallicity. We conclude that the observed FUV emission from metal-rich clusters in M31, M81 and M87 provides evidence that He-enhanced second populations, similar to those observed directly in the Milky Way, may be a ubiquitous feature of globular clusters in the local Universe. Future HST FUV photometry is required to both confirm our interpretation of these archival data and provide constraints on He-enriched second populations of stars in extragalactic globular clusters.

  16. Globular Cluster Contributions to the Galactic Halo

    NASA Astrophysics Data System (ADS)

    Martell, Sarah; Grebel, Eva; Lai, David

    2010-08-01

    The goal of this project is to confirm chemically that globular clusters are the source of as much as half the population of the Galactic halo. Using moderate-resolution spectroscopy from the SEGUE survey, we have identified a previously unknown population of halo field giants with distinctly strong CN features. CN variations are typically only observed in globular clusters, so these stars are interpreted as immigrants to the halo that originally formed in globular clusters. In one night of Keck/HIRES time, we will obtain high-quality, high- resolution spectra for five such stars, and determine abundances of O, Na, Mg, Al, alpha, iron-peak and neutron-capture elements. With this information we can state clearly whether these unusual CN-strong halo stars carry the full abundance pattern seen in CN-strong globular cluster stars, with depleted C, O, and Mg and enhanced N, Na, and Al. This type of coarse ``chemical tagging'' will allow a clearer division of the Galactic halo into contributions from globular clusters and from dwarf galaxies, and will place constraints on theoretical models of globular cluster formation and evolution.

  17. Sampling small-scale and large-scale conformational changes in proteins and molecular complexes

    NASA Astrophysics Data System (ADS)

    Yun, Mi-Ran; Mousseau, N.; Derreumaux, P.

    2007-03-01

    Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.

  18. Differential effect of H1 variant overproduction on gene expression is due to differences in the central globular domain.

    PubMed Central

    Brown, D T; Gunjan, A; Alexander, B T; Sittman, D B

    1997-01-01

    The in vivo overproduction of two mouse histone H1 variants in homologous mouse fibroblasts has opposite effects on gene expression. Overproduction of H1(0) results in repression of transcript levels of all polymerase II genes tested. In contrast, overproduction of H1c results in elevated levels of transcripts. We created a series of chimeric H1 genes in which the regions encoding the three structural domains common to this family of these proteins were systematically switched. Overexpression of these genes in vivo resulted in the accumulation of large amounts of the chimeric H1 in chromatin. Analysis of the effects of overproduction of these proteins revealed that the differential effect of H1 variant overproduction on gene expression is due to differences in the central globular domain. PMID:9396808

  19. Globular adiponectin inhibits ethanol-induced reactive oxygen species production through modulation of NADPH oxidase in macrophages: involvement of liver kinase B1/AMP-activated protein kinase pathway.

    PubMed

    Kim, Mi Jin; Nagy, Laura E; Park, Pil-Hoon

    2014-09-01

    Adiponectin, an adipokine predominantly secreted from adipocytes, has been shown to play protective roles against chronic alcohol consumption. Although excessive reactive oxygen species (ROS) production in macrophages is considered one of the critical events for ethanol-induced damage in various target tissues, the effect of adiponectin on ethanol-induced ROS production is not clearly understood. In the present study, we investigated the effect of globular adiponectin (gAcrp) on ethanol-induced ROS production and the potential mechanisms underlying these effects of gAcrp in macrophages. Here we demonstrated that gAcrp prevented ethanol-induced ROS production in both RAW 264.7 macrophages and primary murine peritoneal macrophages. Globular adiponectin also inhibited ethanol-induced activation of NADPH oxidase. In addition, gAcrp suppressed ethanol-induced increase in the expression of NADPH oxidase subunits, including Nox2 and p22(phox), via modulation of nuclear factor-κB pathway. Furthermore, pretreatment with compound C, a selective inhibitor of AMPK, or knockdown of AMPK by small interfering RNA restored suppression of ethanol-induced ROS production and Nox2 expression by gAcrp. Finally, we found that gAcrp treatment induced phosphorylation of liver kinase B1 (LKB1), an upstream signaling molecule mediating AMPK activation. Knockdown of LKB1 restored gAcrp-suppressed Nox2 expression, suggesting that LKB1/AMPK pathway plays a critical role in the suppression of ethanol-induced ROS production and activation of NADPH oxidase by gAcrp. Taken together, these results demonstrate that globular adiponectin prevents ethanol-induced ROS production, at least in part, via modulation of NADPH oxidase in macrophages. Further, LKB1/AMPK axis plays an important role in the suppression of ethanol-induced NADPH oxidase activation by gAcrp in macrophages.

  20. Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering

    SciTech Connect

    Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A.; Castillo, Amalchi; Chagot, Marie-Eve; Smith, Jarrod A.; Tainer, John A.; Chazin, Walter J.

    2010-03-11

    Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

  1. HUBBLE SPACE TELESCOPE Photometry of the Globular Cluster M4

    NASA Astrophysics Data System (ADS)

    Ibata, Rodrigo A.; Richer, Harvey B.; Fahlman, Gregory G.; Bolte, Michael; Bond, Howard E.; Hesser, James E.; Pryor, Carlton; Stetson, Peter B.

    1999-02-01

    This paper presents a detailed description of the acquisition and processing of a large body of imaging data for three fields in the globular cluster M4 taken with the Wide Field and Planetary Camera 2 aboard the Hubble Space Telescope. Analysis with the ALLFRAME package yielded the deepest photometry yet obtained for this cluster. The resulting data set for 4708 stars (positions and calibrated photometry in V, I, and, in two fields, U) spanning approximately six cluster core radii is presented. The scientific analysis is deferred to three companion papers, which investigate the significant white dwarf population discovered and the main-sequence population.

  2. Globular cluster X-ray sources

    NASA Astrophysics Data System (ADS)

    Pooley, D.

    We know from observations that globular clusters are very efficient catalysts in forming unusual binary systems, such as low-mass X-ray binaries (LMXBs), cataclysmic variables (CVs), and millisecond pulsars (MSPs), with formation rates per unit mass exceeding those in the Galactic disk by orders of magnitude. The high stellar densities in globular clusters trigger various dynamical interactions: exchange encounters, direct collisions, destruction of binaries, and tidal capture. This binary population is, in turn, critical to the stabilization of globular clusters against gravitational collapse; the long-term stability of a cluster is thought to depend on tapping into the gravitational binding energy of such close binaries. I will present an overview of the current state of globular cluster X-ray observations, as well as our work on deep Chandra observations of M4, where we reach some of the lowest X-ray luminosities in any globular cluster (comparable to the deep observations of 47 Tuc and NGC 6397). One of M4 X-ray sources previously classified as a white dwarf binary is likely a neutron star binary, and another X-ray source is a sub-subgiant, the nature of which is still unclear. skip=3pt

  3. Two stellar-mass black holes in the globular cluster M22.

    PubMed

    Strader, Jay; Chomiuk, Laura; Maccarone, Thomas J; Miller-Jones, James C A; Seth, Anil C

    2012-10-04

    Hundreds of stellar-mass black holes probably form in a typical globular star cluster, with all but one predicted to be ejected through dynamical interactions. Some observational support for this idea is provided by the lack of X-ray-emitting binary stars comprising one black hole and one other star ('black-hole/X-ray binaries') in Milky Way globular clusters, even though many neutron-star/X-ray binaries are known. Although a few black holes have been seen in globular clusters around other galaxies, the masses of these cannot be determined, and some may be intermediate-mass black holes that form through exotic mechanisms. Here we report the presence of two flat-spectrum radio sources in the Milky Way globular cluster M22, and we argue that these objects are black holes of stellar mass (each ∼10-20 times more massive than the Sun) that are accreting matter. We find a high ratio of radio-to-X-ray flux for these black holes, consistent with the larger predicted masses of black holes in globular clusters compared to those outside. The identification of two black holes in one cluster shows that ejection of black holes is not as efficient as predicted by most models, and we argue that M22 may contain a total population of ∼5-100 black holes. The large core radius of M22 could arise from heating produced by the black holes.

  4. Large-scale production and protein engineering of G protein-coupled receptors for structural studies

    PubMed Central

    Milić, Dalibor; Veprintsev, Dmitry B.

    2015-01-01

    Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures. PMID:25873898

  5. Large-scale production and protein engineering of G protein-coupled receptors for structural studies.

    PubMed

    Milić, Dalibor; Veprintsev, Dmitry B

    2015-01-01

    Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.

  6. LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

    PubMed

    Adai, Alex T; Date, Shailesh V; Wieland, Shannon; Marcotte, Edward M

    2004-06-25

    Networks are proving to be central to the study of gene function, protein-protein interaction, and biochemical pathway data. Visualization of networks is important for their study, but visualization tools are often inadequate for working with very large biological networks. Here, we present an algorithm, called large graph layout (LGL), which can be used to dynamically visualize large networks on the order of hundreds of thousands of vertices and millions of edges. LGL applies a force-directed iterative layout guided by a minimal spanning tree of the network in order to generate coordinates for the vertices in two or three dimensions, which are subsequently visualized and interactively navigated with companion programs. We demonstrate the use of LGL in visualizing an extensive protein map summarizing the results of approximately 21 billion sequence comparisons between 145579 proteins from 50 genomes. Proteins are positioned in the map according to sequence homology and gene fusions, with the map ultimately serving as a theoretical framework that integrates inferences about gene function derived from sequence homology, remote homology, gene fusions, and higher-order fusions. We confirm that protein neighbors in the resulting map are functionally related, and that distinct map regions correspond to distinct cellular systems, enabling a computational strategy for discovering proteins' functions on the basis of the proteins' map positions. Using the map produced by LGL, we infer general functions for 23 uncharacterized protein families.

  7. NO HEAVY-ELEMENT DISPERSION IN THE GLOBULAR CLUSTER M92

    SciTech Connect

    Cohen, Judith G.

    2011-10-20

    Although there have been recent claims that there is a large dispersion in the abundances of the heavy neutron capture elements in the old Galactic globular cluster M92, we show that the measured dispersion for the absolute abundances of four of the rare earth elements within a sample of 12 luminous red giants in M92 ({<=}0.07 dex) does not exceed the relevant sources of uncertainty. As expected from previous studies, the heavy elements show the signature of the r-process. Their abundance ratios are essentially identical to those of M30, another nearby globular cluster of similar metallicity.

  8. NO EVIDENCE FOR INTERMEDIATE-MASS BLACK HOLES IN GLOBULAR CLUSTERS: STRONG CONSTRAINTS FROM THE JVLA

    SciTech Connect

    Strader, Jay; Chomiuk, Laura; Maccarone, Thomas J.; Miller-Jones, James C. A.; Seth, Anil C.; Heinke, Craig O.; Sivakoff, Gregory R.

    2012-05-10

    With a goal of searching for accreting intermediate-mass black holes (IMBHs), we report the results of ultra-deep Jansky Very Large Array radio continuum observations of the cores of three Galactic globular clusters: M15, M19, and M22. We reach rms noise levels of 1.5-2.1 {mu}Jy beam{sup -1} at an average frequency of 6 GHz. No sources are observed at the center of any of the clusters. For a conservative set of assumptions about the properties of the accretion, we set 3{sigma} upper limits on IMBHs from 360 to 980 M{sub Sun }. These limits are among the most stringent obtained for any globular cluster. They add to a growing body of work that suggests either (1) IMBHs {approx}> 1000 M{sub Sun} are rare in globular clusters or (2) when present, IMBHs accrete in an extraordinarily inefficient manner.

  9. Pixel lensing observations towards globular clusters

    NASA Astrophysics Data System (ADS)

    Cardone, V. F.; Cantiello, M.

    2003-07-01

    It has been suggested that a monitoring program employing the pixel lensing method to search for microlensing events towards galactic globular clusters may increase the statistics and discriminate among different halo models. Stimulated by this proposal, we evaluate an upper limit to the pixel lensing event rate for such a survey. Four different dark halo models have been considered changing both the flattening and the slope of the mass density profile. The lens mass function has been modelled as a homogenous power - law for mu in (mul, muu) and both the mass limits and the slope of the mass function have been varied to investigate their effect on the rate. The target globular clusters have been selected in order to minimize the disk contribution to the event rate. We find that a pixel lensing survey towards globular clusters is unable to discriminate among different halo models since the number of detectable events is too small to allow any reliable statistical analysis.

  10. Globular Cluster Messier 2 in Aquarius

    NASA Technical Reports Server (NTRS)

    2003-01-01

    This image of the Globular cluster Messier 2 (M2) was taken by Galaxy Evolution Explorer on August 20, 2003. This image is a small section of a single All Sky Imaging Survey exposure of only 129 seconds in the constellation Aquarius. This picture is a combination of Galaxy Evolution Explorer images taken with the far ultraviolet (colored blue) and near ultraviolet detectors (colored red). Globular clusters are gravitationally bound systems of hundreds of thousands of stars that orbit in the halos of galaxies. The globular clusters in out Milky Way galaxy contain some of the oldest stars known. M2 lies 33,000 light years from our Sun with stars distributed in a spherical system with a radius of approximately 100 light years.

  11. Large-scale screening for novel low-affinity extracellular protein interactions

    PubMed Central

    Bushell, K. Mark; Söllner, Christian; Schuster-Boeckler, Benjamin; Bateman, Alex; Wright, Gavin J.

    2008-01-01

    Extracellular protein–protein interactions are essential for both intercellular communication and cohesion within multicellular organisms. Approximately a fifth of human genes encode membrane-tethered or secreted proteins, but they are largely absent from recent large-scale protein interaction datasets, making current interaction networks biased and incomplete. This discrepancy is due to the unsuitability of popular high-throughput methods to detect extracellular interactions because of the biochemical intractability of membrane proteins and their interactions. For example, cell surface proteins contain insoluble hydrophobic transmembrane regions, and their extracellular interactions are often highly transient, having half-lives of less than a second. To detect transient extracellular interactions on a large scale, we developed AVEXIS (avidity-based extracellular interaction screen), a high-throughput assay that overcomes these technical issues and can detect very transient interactions (half-lives ≤ 0.1 sec) with a low false-positive rate. We used it to systematically screen for receptor–ligand pairs within the zebrafish immunoglobulin superfamily and identified novel ligands for both well-known and orphan receptors. Genes encoding receptor–ligand pairs were often clustered phylogenetically and expressed in the same or adjacent tissues, immediately implying their involvement in similar biological processes. Using AVEXIS, we have determined the first systematic low–affinity extracellular protein interaction network, supported by independent biological data. This technique will now allow large-scale extracellular protein interaction mapping in a broad range of experimental contexts. PMID:18296487

  12. Millisecond radio pulsars in globular clusters

    NASA Astrophysics Data System (ADS)

    Verbunt, Frank; Lewin, Walter H. G.; van Paradijs, Jan

    1989-04-01

    It is shown that the number of millisecond radio pulsars, in globular clusters, should be larger than 100, applying the standard scenario that all the pulsars descend from low-mass X-ray binaries. Moreover, most of the pulsars are located in a small number of clusters. The prediction that Teran 5 and Liller 1 contain at least about a dozen millisecond radio pulsars each is made. The observations of millisecond radio pulsars in globular clusters to date, in particular the discovery of two millisecond radio pulsars in 47 Tuc, are in agreement with the standard scenario, in which the neutron star is spun up during the mass transfer phase.

  13. Millisecond radio pulsars in globular clusters

    NASA Astrophysics Data System (ADS)

    Verbunt, Frank; Lewin, Walter H. G.; van Paradijs, Jan

    1989-11-01

    It is shown that the number of millisecond radio pulsars, in globular clusters, should be larger than 100, applying the standard scenario that all the pulsars descend from low-mass X-ray binaries. Moreover, most of the pulsars are located in a small number of clusters. The prediction that Teran 5 and Liller 1 contain at least about a dozen millisecond radio pulsars each is made. The observations of millisecond radio pulsars in globular clusters to date, in particular the discovery of two millisecond radio pulsars in 47 Tuc, are in agreement with the standard scenario, in which the neutron star is spun up during the mass transfer phase.

  14. Millisecond radio pulsars in globular clusters

    NASA Technical Reports Server (NTRS)

    Verbunt, Frank; Lewin, Walter H. G.; Vanparadijs, Jan

    1989-01-01

    It is shown that the number of millisecond radio pulsars, in globular clusters, should be larger than 100, applying the standard scenario that all the pulsars descend from low-mass X-ray binaries. Moreover, most of the pulsars are located in a small number of clusters. The prediction that Teran 5 and Liller 1 contain at least about a dozen millisecond radio pulsars each is made. The observations of millisecond radio pulsars in globular clusters to date, in particular the discovery of two millisecond radio pulsars in 47 Tuc, are in agreement with the standard scenario, in which the neutron star is spun up during the mass transfer phase.

  15. Globular adiponectin enhances invasion in human breast cancer cells

    PubMed Central

    FALK LIBBY, EMILY; LIU, JIANZHONG; LI, YI; LEWIS, MONICA J.; DEMARK-WAHNEFRIED, WENDY; HURST, DOUGLAS R.

    2016-01-01

    Every year, a large number of women succumb to metastatic breast cancer due to a lack of curative approaches for this disease. Adiponectin (AdipoQ) is the most abundant of the adipocyte-secreted adipokines. In recent years, there has been an interest in the use of AdipoQ and AdipoQ receptor agonists as therapeutic agents for the treatment of breast cancer. However, while multiple epidemiological studies have previously indicated that low levels of circulating plasma AdipoQ portend poor prognosis in patients with breast cancer, recent studies have reported that elevated expression levels of AdipoQ in breast tissue are correlated with advanced stages of the disease. Thus, the aim of the present study was to clarify the mechanism by which AdipoQ in breast tissue acts directly on tumor cells to regulate the early steps of breast cancer metastasis. In the present study, the effects of different AdipoQ isoforms on the metastatic potential of human breast cancer cells were investigated. The results revealed that globular adiponectin (gAd) promoted invasive cell morphology and significantly increased the migration and invasion abilities of breast cancer cells, whereas full-length adiponectin (fAd) had no effect on these cells. Additionally, gAd, but not fAd, increased the expression levels of microtubule-associated protein 1 light chain 3 beta (LC3B)-II and intracellular LC3B puncta, which are indicators of autophagosome formation, thus suggesting autophagic induction by gAd. Furthermore, the inhibition of autophagic function by autophagy-related protein 7 knockdown attenuated the gAd-induced increase in invasiveness in breast cancer cells. Therefore, the results of the present study suggested that a specific AdipoQ isoform may enhance breast cancer invasion, possibly via autophagic induction. Understanding the roles of the different AdipoQ isoforms as microenvironmental regulatory molecules may aid the development of effective AdipoQ-based treatments for breast cancer

  16. STRUCTURE AND DYNAMICS OF THE GLOBULAR CLUSTER PALOMAR 13

    SciTech Connect

    Bradford, J. D.; Geha, M.; Munoz, R. R.; Santana, F. A.; Simon, J. D.; Cote, P.; Stetson, P. B.; Kirby, E.; Djorgovski, S. G. E-mail: marla.geha@yale.edu

    2011-12-20

    We present Keck/DEIMOS spectroscopy and Canada-France-Hawaii Telescope/MegaCam photometry for the Milky Way globular cluster Palomar 13. We triple the number of spectroscopically confirmed members, including many repeat velocity measurements. Palomar 13 is the only known globular cluster with possible evidence for dark matter, based on a Keck/High Resolution Echelle Spectrometer 21 star velocity dispersion of {sigma} = 2.2 {+-} 0.4 km s{sup -1}. We reproduce this measurement, but demonstrate that it is inflated by unresolved binary stars. For our sample of 61 stars, the velocity dispersion is {sigma} = 0.7{sup +0.6}{sub -0.5} km s{sup -1}. Combining our DEIMOS data with literature values, our final velocity dispersion is {sigma} = 0.4{sup +0.4}{sub -0.3} km s{sup -1}. We determine a spectroscopic metallicity of [Fe/H] = -1.6 {+-} 0.1 dex, placing a 1{sigma} upper limit of {sigma}{sub [Fe/H]} {approx} 0.2 dex on any internal metallicity spread. We determine Palomar 13's total luminosity to be M{sub V} = -2.8 {+-} 0.4, making it among the least luminous known globular clusters. The photometric isophotes are regular out to the half-light radius and mildly irregular outside this radius. The outer surface brightness profile slope is shallower than typical globular clusters ({Sigma}{proportional_to}r{sup {eta}}, {eta} = -2.8 {+-} 0.3). Thus at large radius, tidal debris is likely affecting the appearance of Palomar 13. Combining our luminosity with the intrinsic velocity dispersion, we find a dynamical mass of M{sub 1/2} = 1.3{sup +2:7}{sub -1.3} Multiplication-Sign 10{sup 3} M{sub Sun} and a mass-to-light ratio of M/L{sub V} = 2.4{sup +5.0}{sub -2.4} M{sub Sun }/L{sub Sun }. Within our measurement errors, the mass-to-light ratio agrees with the theoretical predictions for a single stellar population. We conclude that, while there is some evidence for tidal stripping at large radius, the dynamical mass of Palomar 13 is consistent with its stellar mass and neither

  17. Structure and Dynamics of the Globular Cluster Palomar 13

    NASA Astrophysics Data System (ADS)

    Bradford, J. D.; Geha, M.; Muñoz, R. R.; Santana, F. A.; Simon, J. D.; Côté, P.; Stetson, P. B.; Kirby, E.; Djorgovski, S. G.

    2011-12-01

    We present Keck/DEIMOS spectroscopy and Canada-France-Hawaii Telescope/MegaCam photometry for the Milky Way globular cluster Palomar 13. We triple the number of spectroscopically confirmed members, including many repeat velocity measurements. Palomar 13 is the only known globular cluster with possible evidence for dark matter, based on a Keck/High Resolution Echelle Spectrometer 21 star velocity dispersion of σ = 2.2 ± 0.4 km s-1. We reproduce this measurement, but demonstrate that it is inflated by unresolved binary stars. For our sample of 61 stars, the velocity dispersion is σ = 0.7+0.6 -0.5 km s-1. Combining our DEIMOS data with literature values, our final velocity dispersion is σ = 0.4+0.4 -0.3 km s-1. We determine a spectroscopic metallicity of [Fe/H] = -1.6 ± 0.1 dex, placing a 1σ upper limit of σ[Fe/H] ~ 0.2 dex on any internal metallicity spread. We determine Palomar 13's total luminosity to be MV = -2.8 ± 0.4, making it among the least luminous known globular clusters. The photometric isophotes are regular out to the half-light radius and mildly irregular outside this radius. The outer surface brightness profile slope is shallower than typical globular clusters (Σvpropr η, η = -2.8 ± 0.3). Thus at large radius, tidal debris is likely affecting the appearance of Palomar 13. Combining our luminosity with the intrinsic velocity dispersion, we find a dynamical mass of M 1/2 = 1.3+2: 7 -1.3 × 103 M ⊙ and a mass-to-light ratio of M/LV = 2.4+5.0 -2.4 M ⊙/L ⊙. Within our measurement errors, the mass-to-light ratio agrees with the theoretical predictions for a single stellar population. We conclude that, while there is some evidence for tidal stripping at large radius, the dynamical mass of Palomar 13 is consistent with its stellar mass and neither significant dark matter, nor extreme tidal heating, is required to explain the cluster dynamics. The data presented herein were obtained at the W. M. Keck Observatory, which is operated as a

  18. Formation and evolution of clumpy tidal tails in globular clusters

    NASA Astrophysics Data System (ADS)

    Di Matteo, P.; Miocchi, P.; Capuzzo Dolcetta, R.

    2004-05-01

    Numerical simulations of a globular cluster orbiting in the central region of a triaxial galaxy have been performed, in order to study the formation and subsequent evolution of tidal tails and their main features. Tails begin to form after about a quarter of the cluster orbital period and tend to lie along its orbit, with a leading tail that precedes the cluster and an outer tail that trails behind it. Tails show clumpy substructures; the most prominent ones (for a globular cluster moving on a quasi-circular orbit around the galaxy) are located at a distance from the cluster center between 50 pc and 80 pc and, after 3 orbital periods, contain about 10% of the cluster mass at that epoch. The morphology of tails and clumps will be compared with available observational data, in particular with that concerning Palomar 5, for which evident clumps in the tails have been detected. Kinematical properties of stars in the tails (line-of-sight velocities and velocity dispersion profiles) will be presented and compared to kinematical data of M15 and ω Centauri, two galactic globular clusters for which there is evidence that the velocity dispersion remains constant at large radii. All the simulations have been performed with our own implementation of a tree-code, that uses a multipolar expansion of the potential truncated at the quadrupole moment and that ran on high performance computers employing an original parallelization approach implemented via MPI routines. The time-integration of the `particles' trajectories is performed by a 2nd order leap-frog algorithm, using individual and variable time-steps. Part of this work has been done using the IBM SP4 platform located at CINECA (Bologna, Italy) thanks to the grant inarm007 obtained in the framework of INAF-CINECA agreements.

  19. The Trigonometric Parallax of the Globular Cluster M4

    NASA Astrophysics Data System (ADS)

    Rees, Richard F.; Cudworth, Kyle M.

    2017-01-01

    We have identified five stars from the Tycho-Gaia Astrometric Solution catalog as highly probable members of the globular cluster M4 (NGC 6121). A weighted average of the parallax of these five stars results in a cluster parallax of 0.55 ± 0.14 mas, corresponding to a distance of 1.82 ± 0.46 kpc and an absolute distance modulus of 11.30 ± 0.55. Examination of the Gaia DR1 astrometric validation maps of Lindegren et al. (2016) suggests that the systematic errors they identify are likely to be less than 0.1 mas for the immediate region near M4. The reddest of the five stars is also the most distant from the cluster center. This star is somewhat discrepant in both parallax and proper motion compared to the other four. Excluding this star gives a cluster parallax of 0.50 ± 0.15 mas, corresponding to a distance of 2.01 ± 0.62 kpc and an absolute distance modulus of 11.52 ± 0.67. The good agreement with previous measurements of the distance to M4 indicates that either the systematic errors are small or that diverse distance measurement techniques are seriously flawed. While the uncertainties at this point are too large to decide between the differing ground-based distance determinations, the results at this early stage bode well for future globular cluster parallaxes from Gaia. To our knowledge, this is the first measurement of the trigonometric parallax of a globular cluster.

  20. Tidal Densities of Globular Clusters and the Galactic Mass Distribution

    NASA Astrophysics Data System (ADS)

    Lee, Hyung Mok

    1990-12-01

    The tidal radii of globular clusters reflect the tidal field of the Galaxy. The mass distribution of the Galaxy thus may be obtained if the tidal fields of clusters are well known. Although large amounts of uncertainties in the determination of tidal radii have been obstacles in utilizing this method, analysis of tidal density could give independent check for the Galactic mass distribution. Recent theoretical modeling of dynamical evolution including steady Galactic tidal field shows that the observationally determined tidal radii could be systematically larger by about a factor of 1.5 compared to the theoretical values. From the analysis of entire sample of 148 globular clusters and 7 dwarf spheroidal systems compiled by Webbink(1985), we find that such reduction from observed values would make the tidal density(the mean density within the tidal radius) distribution consistent with the flat rotation curve of our Galaxy out to large distances if the velocity distribution of clusters and dwarf spheroidals with respect to the Galactic center is isotropic.

  1. A coclustering approach for mining large protein-protein interaction networks.

    PubMed

    Pizzuti, Clara; Rombo, Simona E

    2012-01-01

    Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonoverlapping clusters. The density of the clusters to search for can also be set by the user. We tested our method on the two networks of yeast and human, and compared it to other five well-known techniques on the same interaction data sets. The results showed that, for all the examples considered, our approach always reaches a good compromise between accuracy and network coverage. Furthermore, the behavior of our algorithm is not influenced by the structure of the input network, different from all the techniques considered in the comparison, which returned very good results on the yeast network, while on the human network their outcomes are rather poor.

  2. The fundamental plane correlations for globular clusters

    NASA Technical Reports Server (NTRS)

    Djorgovski, S.

    1995-01-01

    In the parameter space whose axes include a radius (core, or half-light), a surface brightness (central, or average within the half-light radius), and the central projected velocity dispersion, globular clusters lie on a two-dimensional surface (a plane, if the logarithmic quantities are used). This is analogous to the 'fundamental plane' of elliptical galaxies. The implied bivariate correlations are the best now known for globular clusters. The derived scaling laws for the core properties imply that cluster cores are fully virialized, homologous systems, with a constant (M/L) ratio. The corresponding scaling laws on the half-light scale are differrent, but are nearly identical to those derived from the 'fundamental plane' of ellipticals. This may be due to the range of cluster concentrations, which are correlated with other parameters. A similar explanation for elliptical galaxies may be viable. These correlations provide new empirical constraints for models of globular cluster formation and evolution, and may also be usable as rough distance-indicator relations for globular clusters.

  3. A black hole in a globular cluster.

    PubMed

    Maccarone, Thomas J; Kundu, Arunav; Zepf, Stephen E; Rhode, Katherine L

    2007-01-11

    Globular star clusters contain thousands to millions of old stars packed within a region only tens of light years across. Their high stellar densities make it very probable that their member stars will interact or collide. There has accordingly been considerable debate about whether black holes should exist in these star clusters. Some theoretical work suggests that dynamical processes in the densest inner regions of globular clusters may lead to the formation of black holes of approximately 1,000 solar masses. Other numerical simulations instead predict that stellar interactions will eject most or all of the black holes that form in globular clusters. Here we report the X-ray signature of an accreting black hole in a globular cluster associated with the giant elliptical galaxy NGC 4472 (in the Virgo cluster). This object has an X-ray luminosity of about 4 x 10(39) erg s(-1), which rules out any object other than a black hole in such an old stellar population. The X-ray luminosity varies by a factor of seven in a few hours, which excludes the possibility that the object is several neutron stars superposed.

  4. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

    PubMed Central

    Abdallah, Bahige G.; Kupitz, Christopher; Fromme, Petra; Ros, Alexandra

    2014-01-01

    Traditional macroscale protein crystallization is accomplished non-trivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time consuming and resource intensive, hindering protein structure determination. Even more difficulties arise when crystallizing large membrane protein complexes such as photosystem I (PSI) due to their large unit cells dominated by solvent and complex characteristics that call for even stricter buffer requirements. Structure determination techniques tailored for these ‘difficult to crystallize’ proteins such as femtosecond nanocrystallography are being developed, yet still need specific crystal characteristics. Here, we demonstrate a simple and robust method to screen protein crystallization conditions at low ionic strength in a microfluidic device. This is realized in one microfluidic experiment using low sample amounts, unlike traditional methods where each solution condition is set up separately. Second harmonic generation microscopy via Second Order Nonlinear Imaging of Chiral Crystals (SONICC) was applied for the detection of nanometer and micrometer sized PSI crystals within microchannels. To develop a crystallization phase diagram, crystals imaged with SONICC at specific channel locations were correlated to protein and salt concentrations determined by numerical simulations of the time-dependent diffusion process along the channel. Our method demonstrated that a portion of the PSI crystallization phase diagram could be reconstructed in excellent agreement with crystallization conditions determined by traditional methods. We postulate that this approach could be utilized to efficiently study and optimize crystallization conditions for a wide range of proteins that are poorly understood to date. PMID:24191698

  5. MLL2 protein is a prognostic marker for gastrointestinal diffuse large B-cell lymphoma

    PubMed Central

    Ye, Haige; Lu, Lu; Ge, Bei; Gao, Shenmeng; Ma, Yongyong; Liang, Bin; Yu, Kang; Yang, Kaiyan

    2015-01-01

    Mixed linage leukemia gene 2 (MLL2) is identified as a novel mutation gene in diffuse large B cell lymphoma (DLBCL). However, the significance of MLL2 protein expression for the prognosis of DLBCL is unclear. In this study, we detected MLL2 protein expression in primary gastrointestinal diffuse large B cell lymphoma (PGI-DLBCL) samples by using tissue microarray immunohistochemistry, and analyzed the correlation between MLL2 protein expression and tumor proliferation activity. In addition, we investigated clinical significance of MLL2 protein expression for PGI-DLBCL prognosis. We found that there was significant difference in MLL2 protein expression between PGI-DLBCL and reactive hyperplasia of lymph node. High expression of MLL2 protein indicated higher clinical stage. In older patients (>60 years) with PGI-DLBCL, MLL2 protein expression was positively correlated with Ki-67 expression and negatively correlated with patient survival. Our data suggest that MLL2 protein is overexpressed in PGI-DLBCL and appears as a prognostic factor for patients of PGI-DLBCL, especially for those older than 60 years old. PMID:26722499

  6. Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering.

    PubMed

    Cai, Xiao-Hui; Jaroszewski, Lukasz; Wooley, John; Godzik, Adam

    2011-08-01

    The protein universe can be organized in families that group proteins sharing common ancestry. Such families display variable levels of structural and functional divergence, from homogenous families, where all members have the same function and very similar structure, to very divergent families, where large variations in function and structure are observed. For practical purposes of structure and function prediction, it would be beneficial to identify sub-groups of proteins with highly similar structures (iso-structural) and/or functions (iso-functional) within divergent protein families. We compared three algorithms in their ability to cluster large protein families and discuss whether any of these methods could reliably identify such iso-structural or iso-functional groups. We show that clustering using profile-sequence and profile-profile comparison methods closely reproduces clusters based on similarities between 3D structures or clusters of proteins with similar biological functions. In contrast, the still commonly used sequence-based methods with fixed thresholds result in vast overestimates of structural and functional diversity in protein families. As a result, these methods also overestimate the number of protein structures that have to be determined to fully characterize structural space of such families. The fact that one can build reliable models based on apparently distantly related templates is crucial for extracting maximal amount of information from new sequencing projects.

  7. Health Benefits of Texturized Whey Proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whey proteins are an important class of food ingredients used in many functional foods to boost protein content. Using the extrusion texturization process to partially open the native globular structures of whey proteins changed their conformation to the molten globular state, resulting in a new cla...

  8. Bayesian Analysis and Characterization of Multiple Populations in Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Wagner-Kaiser, Rachel A.; Stenning, David; Sarajedini, Ata; von Hippel, Ted; van Dyk, David A.; Robinson, Elliot; Stein, Nathan; Jefferys, William H.; BASE-9, HST UVIS Globular Cluster Treasury Program

    2017-01-01

    Globular clusters have long been important tools to unlock the early history of galaxies. Thus, it is crucial we understand the formation and characteristics of the globular clusters (GCs) themselves. Historically, GCs were thought to be simple and largely homogeneous populations, formed via collapse of a single molecular cloud. However, this classical view has been overwhelmingly invalidated by recent work. It is now clear that the vast majority of globular clusters in our Galaxy host two or more chemically distinct populations of stars, with variations in helium and light elements at discrete abundance levels. No coherent story has arisen that is able to fully explain the formation of multiple populations in globular clusters nor the mechanisms that drive stochastic variations from cluster to cluster.We use Cycle 21 Hubble Space Telescope (HST) observations and HST archival ACS Treasury observations of 30 Galactic Globular Clusters to characterize two distinct stellar populations. A sophisticated Bayesian technique is employed to simultaneously sample the joint posterior distribution of age, distance, and extinction for each cluster, as well as unique helium values for two populations within each cluster and the relative proportion of those populations. We find the helium differences among the two populations in the clusters fall in the range of 0.04 to 0.11. Because adequate models varying in CNO are not presently available, we view these spreads as upper limits and present them with statistical rather than observational uncertainties. Evidence supports previous studies suggesting an increase in helium content concurrent with increasing mass of the cluster. We also find that the proportion of the first population of stars increases with mass. Our results are examined in the context of proposed globular cluster formation scenarios.

  9. Manganese Abundances in Globular Cluster and Halo Field Stars

    NASA Astrophysics Data System (ADS)

    Sobeck, J. S.; Simmerer, J. A.; Fulbright, J. P.; Sneden, C.; Kraft, R. P.; Ivans, I. I.

    2004-05-01

    We have derived Mn abundances for more than 100 stars in nine Galactic globular clusters: M3, M4, M5, M10, M13, M15, M71, Pal5 and NGC 7006. In addition, Mn abundance determinations have been made for a comparable number of halo field stars possessing an overlapping range of metallicities and stellar parameters. The spectra of the cluster giants were obtained as a part of the Lick-Texas investigations into globular cluster chemistry. The spectra of the field stars are a part of a large study by Simmerer et al. (2004, ApJ, submitted). Data were collected at the McDonald, Lick ,and Keck Observatories and were analyzed using the synthetic spectra of the 6000 Å Mn I triplet. Hyperfine structure parameters were included in the synthetic spectra computations. It is well known that metal-poor field stars possess [Mn/Fe] ratios approximately a factor of two lower than solar values (Wallerstein et al. 1963, Gratton et al.1989, McWilliam et al. 1997). Our analysis shows that for the metallicity range -0.5 > [Fe/H] > -2.8 field stars have a mean relative abundance of <[Mn/Fe]> = -0.28±0.01 (sigma = 0.08), a value esssentially identical to that of the nine globular clusters: <[Mn/Fe]> = -0.28±0.01 (sigma = 0.12). It is evident that [Mn/Fe] ratios of metal-poor stars do not depend upon their environment. Our Mn abundance results viewed in conjunction with the globular cluster Cu abundances of Simmerer et al. (2003) suggest the following possibilities: one, the production of these elements is extremely metallicity-dependent or two, these elements were manufactured in the Galactic halo prior to cluster formation. Ongoing support from NSF, currently through grants AST-0307495 to CS and AST-0098453 to RPK, is gratefully acknowledged. Research for III is currently supported by NASA through Hubble Fellowship grant HST-HF-01151.01-A from the Space Telescope Science Institute.

  10. Sulfur in the globular clusters 47 Tucanae and NGC 6752

    NASA Astrophysics Data System (ADS)

    Sbordone, L.; Limongi, M.; Chieffi, A.; Caffau, E.; Ludwig, H.-G.; Bonifacio, P.

    2009-08-01

    Context: The light elements Li, O, Na, Al, and Mg are known to show star-to-star variations in the globular clusters 47 Tuc and NGC 6752. Such variations are interpreted as coming from processing in a previous generation of stars. Aims: In this paper we investigate the abundances of the α-element sulfur, for which no previous measurements exist. In fact this element has not been investigated in any Galactic globular cluster so far. The only globular cluster for which such measurements are available is Terzan 7, which belongs to the Sgr dSph. Methods: We use high-resolution spectra of the S i Mult. 1, acquired with the UVES spectrograph at the 8.2 m VLT-Kueyen telescope, for turn-off and giant stars in the two globular clusters. The spectra were analysed making use of ATLAS static plane parallel model atmospheres and SYNTHE spectrum synthesis. We also compute 3D corrections from CO^5BOLD hydrodynamic models and apply corrections due to NLTE effects taken from the literature. Results: In the cluster NGC 6752 sulfur has been measured only in four subgiant stars. We find no significant star-to-star scatter and a mean <[S/Fe]> = +0.49 ± 0.15, consistent with what is observed in field stars of the same metallicity. In the cluster 47 Tuc we measured S in 4 turn-off and 5 subgiant stars with a mean <[S/Fe]> = +0.18 ± 0.14. While this result is compatible with no star-to-star scatter we notice a statistically significant correlation of the sulfur abundance with the sodium abundance and a tentative correlation with the silicon abundance. Conclusions: The sulfur-sodium correlation is not easily explained in terms of nucleosynthesis. An origin due to atomic diffusion can be easily dismissed. The correlation cannot be easily dismissed either, in view of its statistical significance, until better data for more stars is available. Based on observations made with the ESO VLT-Kueyen telescope at the Paranal Observatory, Chile, in the course of the ESO-Large Programme 165.L-0263.

  11. A Large-Scale Quantitative Proteomic Approach To Identifying Sulfur Mustard-Induced Protein Phosphorylation Cascades

    DTIC Science & Technology

    2009-07-31

    with immobilized metal affinity chromatography to study the large-scale protein phosphorylation changes resulting from SM exposure in a human...medium, resulting in isotopically “light” and “ heavy ” cell populations, respectively. Protein samples collected from control (light-labeled) and...experimental ( heavy -labeled) cells can then be mixed in equal ratios, digested with trypsin, and analyzed by high-resolution mass spectrometry. The

  12. Globular cluster x-ray sources.

    PubMed

    Pooley, David

    2010-04-20

    Globular clusters and x-ray astronomy have a long and fruitful history. Uhuru and OSO-7 revealed highly luminous (> 10(36) ergs(-1)) x-ray sources in globular clusters, and Einstein and ROSAT revealed a larger population of low-luminosity (< 10(33) ergs(-1)) x-ray sources. It was realized early on that the high-luminosity sources were low-mass x-ray binaries in outburst and that they were orders of magnitude more abundant per unit mass in globular clusters than in the rest of the galaxy. However, the low-luminosity sources proved difficult to classify. Many ideas were put forth--low-mass x-ray binaries in quiescence (qLMXBs), cataclysmic variables (CVs), active main-sequence binaries (ABs), and millisecond pulsars (MSPs)--but secure identifications were scarce. In ROSAT observations of 55 clusters, about 25 low-luminosity sources were found. Chandra has now observed over 80 Galactic globular clusters, and these observations have revealed over 1,500 x-ray sources. The superb angular resolution has allowed for many counterpart identifications, providing clues to the nature of this population. It is a heterogeneous mix of qLMXBs, CVs, ABs, and MSPs, and it has been shown that the qLMXBs and CVs are both, in part, overabundant like the luminous LMXBs. The number of x-ray sources in a cluster correlates very well with its encounter frequency. This points to dynamical formation scenarios for the x-ray sources and shows them to be excellent tracers of the complicated internal dynamics. The relation between the encounter frequency and the number of x-ray sources has been used to suggest that we have misunderstood the dynamical states of globular clusters.

  13. Mesoporous Silica Nanoparticles with Large Pores for the Encapsulation and Release of Proteins.

    PubMed

    Tu, Jing; Boyle, Aimee L; Friedrich, Heiner; Bomans, Paul H H; Bussmann, Jeroen; Sommerdijk, Nico A J M; Jiskoot, Wim; Kros, Alexander

    2016-11-30

    Mesoporous silica nanoparticles (MSNs) have been explored extensively as solid supports for proteins in biological and medical applications. Small (<200 nm) MSNs with ordered large pores (>5 nm), capable of encapsulating therapeutic small molecules suitable for delivery applications in vivo, are rare however. Here we present small, elongated, cuboidal, MSNs with average dimensions of 90 × 43 nm that possess disk-shaped cavities, stacked on top of each other, which run parallel to the short axis of the particle. Amine functionalization was achieved by modifying the MSN surface with 3-aminopropyltriethoxysilane or 3-[2-(2-aminoethylamino)ethylamino]propyltrimethoxysilane (AP-MSNs and AEP-MSNs) and were shown to have similar dimensions to the nonfunctionalized MSNs. The dimensions of these particles, and their large surface areas as measured by nitrogen adsorption-desorption isotherms, make them ideal scaffolds for protein encapsulation and delivery. We therefore investigated the encapsulation and release behavior for seven model proteins (α-lactalbumin, ovalbumin, bovine serum albumin, catalase, hemoglobin, lysozyme, and cytochrome c). It was discovered that all types of MSNs used in this study allow rapid encapsulation, with a high loading capacity, for all proteins studied. Furthermore, the release profiles of the proteins were tunable. The variation in both rate and amount of protein uptake and release was found to be determined by the surface chemistry of the MSNs, together with the isoelectric point (pI), and molecular weight of the proteins, as well as by the ionic strength of the buffer. These MSNs with their large surface area and optimal dimensions provide a scaffold with a high encapsulation efficiency and controllable release profiles for a variety of proteins, enabling potential applications in fields such as drug delivery and protein therapy.

  14. BCSearch: fast structural fragment mining over large collections of protein structures.

    PubMed

    Guyon, Frédéric; Martz, François; Vavrusa, Marek; Bécot, Jérôme; Rey, Julien; Tufféry, Pierre

    2015-07-01

    Resources to mine the large amount of protein structures available today are necessary to better understand how amino acid variations are compatible with conformation preservation, to assist protein design, engineering and, further, the development of biologic therapeutic compounds. BCSearch is a versatile service to efficiently mine large collections of protein structures. It relies on a new approach based on a Binet-Cauchy kernel that is more discriminative than the widely used root mean square deviation criterion. It has statistics independent of size even for short fragments, and is fast. The systematic mining of large collections of structures such as the complete SCOPe protein structural classification or comprehensive subsets of the Protein Data Bank can be performed in few minutes. Based on this new score, we propose four innovative applications: BCFragSearch and BCMirrorSearch, respectively, search for fragments similar and anti-similar to a query and return information on the diversity of the sequences of the hits. BCLoopSearch identifies candidate fragments of fixed size matching the flanks of a gaped structure. BCSpecificitySearch analyzes a complete protein structure and returns information about sites having few similar fragments. BCSearch is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/BCSearch.

  15. Strategy for large scale solubilization of coal - characterization of Neurospora protein and gene

    SciTech Connect

    Patel, A.; Chen, Y.P.; Mishra, N.C.

    1995-12-31

    Low grade coal placed on mycelial mat of Neurospora crassa growing on Petri plate was found to be solubilized by this fungus. A heat stable protein has been purified to near homogeneity which can solubilize low grade coal in in vitro. The biochemical properties of the Neurospora protein will be presented. The nature of the product obtained after solubilization of coal by Neurospora protein in vivo and in vitro will also be presented. The N-terminus sequence of the amino acids of this protein will be used to design primer for possible cloning of gene for Neurospora protein capable of solubilization of coal in order to develop methodology for coal solubilization on a large scale.

  16. Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

    NASA Astrophysics Data System (ADS)

    Yu, Garmay; A, Shvetsov; D, Karelov; D, Lebedev; A, Radulescu; M, Petukhov; V, Isaev-Ivanov

    2012-02-01

    Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

  17. Sequence determines degree of knottedness in a coarse-grained protein model.

    PubMed

    Wüst, Thomas; Reith, Daniel; Virnau, Peter

    2015-01-16

    Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.

  18. Genome-scale phylogenetic function annotation of large and diverse protein families.

    PubMed

    Engelhardt, Barbara E; Jordan, Michael I; Srouji, John R; Brenner, Steven E

    2011-11-01

    The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. Here we present a revised approach (SIFTER version 2.0) that enables annotations on a genomic scale. SIFTER 2.0 produces equivalently precise predictions compared to the earlier version on a carefully studied family and on a collection of 100 protein families. We have added an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0%, and 5.7% of these proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available at http://sifter.berkeley.edu.

  19. THE FIRST CONFIRMED MICROLENS IN A GLOBULAR CLUSTER

    SciTech Connect

    Pietrukowicz, P.; Udalski, A.; Minniti, D.; Alonso-Garcia, J.; Jetzer, Ph.

    2012-01-10

    In 2000 July/August a microlensing event occurred at a distance of 2.'33 from the center of the globular cluster M22 (NGC 6656), observed against the dense stellar field of the Milky Way bulge. We have used the adaptive optics system NACO at the ESO Very Large Telescope to resolve the two objects that participated in the event: the lens and the source. The position of the objects measured in 2011 July is in agreement with the observed relative proper motion of M22 with respect to the background bulge stars. Based on the brightness of the microlens components we find that the source is a solar-type star located at a distance of 6.0 {+-} 1.5 kpc in the bulge, while the lens is a 0.18 {+-} 0.01 M{sub Sun} dwarf member of the globular cluster located at the known distance of 3.2 {+-} 0.2 kpc from the Sun.

  20. Dynamical Evolution of Outer-Halo Globular Clusters

    NASA Astrophysics Data System (ADS)

    Küpper, Andreas H. W.; Zonoozi, Akram H.; Haghi, Hosein; Lützgendorf, Nora; Mieske, Steffen; Frank, Matthias; Baumgardt, Holger; Kroupa, Pavel

    2017-03-01

    Outer-halo globular clusters show large half-light radii and flat stellar mass functions, depleted in low-mass stars. Using N-body simulations of globular clusters on eccentric orbits within a Milky Way-like potential, we show how a cluster's half-mass radius and its mass function develop over time. The slope of the central mass function flattens proportionally to the amount of mass a cluster has lost, and the half-mass radius grows to a size proportional to the average strength of the tidal field. The main driver of these processes is mass segregation of dark remnants. We conclude that the extended, depleted clusters observed in the Milky Way must have had small half-mass radii in the past, and that they expanded due to the weak tidal field they spend most of their lifetime in. Moreover, their mass functions must have been steeper in the past but flattened significantly as a cause of mass segregation and tidal mass loss.

  1. Would a Galactic bar destroy the globular cluster system?

    NASA Technical Reports Server (NTRS)

    Long, Kevin; Ostriker, Jeremiah P.; Aguilar, Luis

    1992-01-01

    Five different dynamical Galaxy models are presented for the Galactic potential which satisfy the observed rotation curve but contain a central bar so that the 3-kpc nonintersecting streamlines have a radial velocity of 50 km/s when viewed at 45 deg to the bar axis. The effect of the central bars on the destruction rates of globular clusters in the Galaxy is investigated. The method of Aguilar et al. (1988) is applied to these barred Galaxy models. The unknown tangential velocity components of each observed cluster are drawn randomly from an assumed distribution function. The cluster's orbit is integrated, and the bulge shocking rate is calculated. The median destruction rate of the cluster is computed by sampling a large number of such orbits. The addition of the rotating bar does not strongly affect the destruction rates of globular clusters. There is a small increase in the destruction rate for those clusters within about 2.5 kpc. Thus it is not possible to rule out the existence of a rotating bar on these grounds.

  2. Formation of Globular Clusters in Hierarchical Cosmology: ART and Science

    NASA Astrophysics Data System (ADS)

    Gnedin, Oleg Y.; Prieto, José L.

    We test the hypothesis that globular clusters form in supergiant molecular clouds within high-redshift galaxies. Numerical simulations demonstrate that such large, dense, and cold gas clouds assemble naturally in current hierarchical models of galaxy formation. These clouds are enriched with heavy elements from earlier stars and could produce star clusters in a similar way to nearby molecular clouds. The masses and sizes of the model clusters are in excellent agreement with the observations of young massive clusters. Do these model clusters evolve into globular clusters that we see in our and external galaxies? In order to study their dynamical evolution, we calculate the orbits of model clusters using the outputs of the cosmological simulation of a Milky Way-sized galaxy. We find that at present the orbits are isotropic in the inner 50 kpc of the Galaxy and preferentially radial at larger distances. All clusters located outside 10 kpc from the center formed in the now-disrupted satellite galaxies. The spatial distribution of model clusters is spheroidal, with a power-law density profile consistent with observations. The combination of two-body scattering, tidal shocks, and stellar evolution results in the evolution of the cluster mass function from an initial power law to the observed log-normal distribution. However, not all initial conditions and not all evolution scenarios are consistent with the observed mass function.

  3. Interactive Effects of Indigestible Carbohydrates, Protein Type, and Protein Level on Biomarkers of Large Intestine Health in Rats

    PubMed Central

    Taciak, Marcin; Barszcz, Marcin; Tuśnio, Anna; Pastuszewska, Barbara

    2015-01-01

    The effects of indigestible carbohydrates, protein type, and protein level on large intestine health were examined in rats. For 21 days, 12 groups of six 12-week-old male Wistar rats were fed diets with casein (CAS), or potato protein concentrate (PPC), providing 14% (lower protein level; LP), or 20% (higher protein level; HP) protein, and containing cellulose, resistant potato starch, or pectin. Fermentation end-products, pH, and β-glucuronidase levels in cecal digesta, and ammonia levels in colonic digesta were determined. Cecal digesta, tissue weights, cecal and colon morphology, and colonocyte DNA damage were also analyzed. Digesta pH was lower, whereas relative mass of cecal tissue and digesta were higher in rats fed pectin diets than in those fed cellulose. Cecal parameters were greater in rats fed PPC and HP diets than in those fed CAS and LP diets, respectively. Short-chain fatty acid (SCFA) concentrations were unaffected by protein or carbohydrate type. Total SCFA, acetic acid, and propionic acid concentrations were greater in rats fed LP diets than in those fed HP. Cecal pool of isobutyric and isovaleric acids was greater in rats fed PPC than in those fed CAS diets. PPC diets decreased phenol concentration and increased ammonia concentration in cecal and colonic digesta, respectively. Cecal crypt depth was greater in rats fed PPC and HP diets, and was unaffected by carbohydrates; whereas colonic crypt depth was greater in rats fed cellulose. Myenteron thickness in the cecum was unaffected by nutrition, but was greater in the colon of rats fed cellulose. Colonocyte DNA damage was greater in rats fed LP diets than in those fed HP diets, and was unaffected by carbohydrate or protein type. It was found that nutritional factors decreasing cecal digesta weight contribute to greater phenol production, increased DNA damage, and reduced ammonia concentration in the colon. PMID:26536028

  4. Approach for growth of high-quality and large protein crystals.

    PubMed

    Matsumura, Hiroyoshi; Sugiyama, Shigeru; Hirose, Mika; Kakinouchi, Keisuke; Maruyama, Mihoko; Murai, Ryota; Adachi, Hiroaki; Takano, Kazufumi; Murakami, Satoshi; Mori, Yusuke; Inoue, Tsuyoshi

    2011-01-01

    Three crystallization methods for growing large high-quality protein crystals, i.e. crystallization in the presence of a semi-solid agarose gel, top-seeded solution growth (TSSG) and a large-scale hanging-drop method, have previously been presented. In this study the effectiveness of crystallization in the presence of a semi-solid agarose gel has been further evaluated by crystallizing additional proteins in the presence of 2.0% (w/v) agarose gel, resulting in complete gelification with high mechanical strength. In TSSG the seed crystals are hung by a seed holder protruding from the top of the growth vessel to prevent polycrystallization. In the large-scale hanging-drop method, a cut pipette tip was used to maintain large-scale droplets consisting of protein-precipitant solution. Here a novel crystallization method that combines TSSG and the large-scale hanging-drop method is reported. A large and single crystal of lysozyme was obtained by this method.

  5. Comparative Proteomics of Mouse Tears and Saliva: Evidence from Large Protein Families for Functional Adaptation

    PubMed Central

    Karn, Robert C.; Laukaitis, Christina M.

    2015-01-01

    We produced a tear proteome of the genome mouse, C57BL/6, that contained 139 different protein identifications: 110 from a two-dimensional (2D) gel with subsequent trypsin digestion, 19 from a one-dimensional (1D) gel with subsequent trypsin digestion and ten from a 1D gel with subsequent Asp-N digestion. We compared this tear proteome with a C57BL/6 mouse saliva proteome produced previously. Sixteen of the 139 tear proteins are shared between the two proteomes, including six proteins that combat microbial growth. Among the 123 other tear proteins, were members of four large protein families that have no counterparts in humans: Androgen-binding proteins (ABPs) with different members expressed in the two proteomes, Exocrine secreted peptides (ESPs) expressed exclusively in the tear proteome, major urinary proteins (MUPs) expressed in one or both proteomes and the mouse-specific Kallikreins (subfamily b KLKs) expressed exclusively in the saliva proteome. All four families have members with suggested roles in mouse communication, which may influence some aspect of reproductive behavior. We discuss this in the context of functional adaptation involving tear and saliva proteins in the secretions of mouse lacrimal and salivary glands, respectively.

  6. Studies on the Assembly Characteristics of Large Subunit Ribosomal Proteins in S. cerevisae

    PubMed Central

    Ohmayer, Uli; Gamalinda, Michael; Sauert, Martina; Ossowski, Julius; Pöll, Gisela; Linnemann, Jan; Hierlmeier, Thomas; Perez-Fernandez, Jorge; Kumcuoglu, Beril; Leger-Silvestre, Isabelle; Faubladier, Marlène; Griesenbeck, Joachim; Woolford, John; Tschochner, Herbert; Milkereit, Philipp

    2013-01-01

    During the assembly process of ribosomal subunits, their structural components, the ribosomal RNAs (rRNAs) and the ribosomal proteins (r-proteins) have to join together in a highly dynamic and defined manner to enable the efficient formation of functional ribosomes. In this work, the assembly of large ribosomal subunit (LSU) r-proteins from the eukaryote S. cerevisiae was systematically investigated. Groups of LSU r-proteins with specific assembly characteristics were detected by comparing the protein composition of affinity purified early, middle, late or mature LSU (precursor) particles by semi-quantitative mass spectrometry. The impact of yeast LSU r-proteins rpL25, rpL2, rpL43, and rpL21 on the composition of intermediate to late nuclear LSU precursors was analyzed in more detail. Effects of these proteins on the assembly states of other r-proteins and on the transient LSU precursor association of several ribosome biogenesis factors, including Nog2, Rsa4 and Nop53, are discussed. PMID:23874617

  7. Simulation guided design of globular single-chain nanoparticles by tuning the solvent quality.

    PubMed

    Lo Verso, Federica; Pomposo, José A; Colmenero, Juan; Moreno, Angel J

    2015-02-04

    The control of primary and further structures of individual folded/collapsed synthetic polymers has received significant attention in recent years. However, the synthesis of single-chain nanoparticles (SCNPs) showing a compact, globular conformation in solution has turned out so far to be highly elusive. By means of simulations, we propose two methods for obtaining globular SCNPs in solution. The first synthesis route is performed in the bad solvent, with the precursor anchored to a surface. In the second route we use a random copolymer precursor with unreactive solvophilic and reactive solvophobic units, which form a single core-shell structure. Both protocols prevent intermolecular cross-linking. After recovering good solvent conditions, the swollen nanoparticles maintain their globular character. The proposed methods are experimentally realizable and do not require specific sequence control of the precursors. Our results pave the way for the synthesis via solvent-assisted design of a new generation of globular soft nanoparticles mimicking global conformations of native proteins in solution.

  8. Genetics of single-cell protein abundance variation in large yeast populations

    NASA Astrophysics Data System (ADS)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  9. Scale-up of isoelectric focusing. [for large scale protein fracionation

    NASA Technical Reports Server (NTRS)

    Bier, Milan

    1986-01-01

    The paper describes some applications to large scale protein fractionation using a recycling isoelectric focusing apparatus. Separation is achieved in free solution without the use of supporting media. Various alternatives for the formation of the pH gradient are discussed and results of a computer simulation are presented.

  10. Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses

    PubMed Central

    Venclovas, Česlovas

    2012-01-01

    Motivation: Eukaryote-infecting nucleo-cytoplasmic large DNA viruses (NCLDVs) feature some of the largest genomes in the viral world. These viruses typically do not strongly depend on the host DNA replication systems. In line with this observation, a number of essential DNA replication proteins, such as DNA polymerases, primases, helicases and ligases, have been identified in the NCLDVs. One other ubiquitous component of DNA replisomes is the single-stranded DNA-binding (SSB) protein. Intriguingly, no NCLDV homologs of canonical OB-fold-containing SSB proteins had previously been detected. Only in poxviruses, one of seven NCLDV families, I3 was identified as the SSB protein. However, whether I3 is related to any known protein structure has not yet been established. Results: Here, we addressed the case of ‘missing’ canonical SSB proteins in the NCLDVs and also probed evolutionary origins of the I3 family. Using advanced computational methods, in four NCLDV families, we detected homologs of the bacteriophage T7 SSB protein (gp2.5). We found the properties of these homologs to be consistent with the SSB function. Moreover, we implicated specific residues in single-stranded DNA binding. At the same time, we found no evolutionary link between the T7 gp2.5-like NCLDV SSB homologs and the poxviral SSB protein (I3). Instead, we identified a distant relationship between I3 and small protein B (SmpB), a bacterial RNA-binding protein. Thus, apparently, the NCLDVs have the two major distinct sets of SSB proteins having bacteriophage and bacterial origins, respectively. Contact: venclovas@ibt.lt Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23097418

  11. Structure and evolutionary history of a large family of NLR proteins in the zebrafish

    PubMed Central

    Zielinski, Julia; Kondrashov, Fyodor

    2016-01-01

    Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system. PMID:27248802

  12. Large-scale Top-down Proteomics of the Human Proteome: Membrane Proteins, Mitochondria, and Senescence*

    PubMed Central

    Catherman, Adam D.; Durbin, Kenneth R.; Ahlf, Dorothy R.; Early, Bryan P.; Fellers, Ryan T.; Tran, John C.; Thomas, Paul M.; Kelleher, Neil L.

    2013-01-01

    Top-down proteomics is emerging as a viable method for the routine identification of hundreds to thousands of proteins. In this work we report the largest top-down study to date, with the identification of 1,220 proteins from the transformed human cell line H1299 at a false discovery rate of 1%. Multiple separation strategies were utilized, including the focused isolation of mitochondria, resulting in significantly improved proteome coverage relative to previous work. In all, 347 mitochondrial proteins were identified, including ∼50% of the mitochondrial proteome below 30 kDa and over 75% of the subunits constituting the large complexes of oxidative phosphorylation. Three hundred of the identified proteins were found to be integral membrane proteins containing between 1 and 12 transmembrane helices, requiring no specific enrichment or modified LC-MS parameters. Over 5,000 proteoforms were observed, many harboring post-translational modifications, including over a dozen proteins containing lipid anchors (some previously unknown) and many others with phosphorylation and methylation modifications. Comparison between untreated and senescent H1299 cells revealed several changes to the proteome, including the hyperphosphorylation of HMGA2. This work illustrates the burgeoning ability of top-down proteomics to characterize large numbers of intact proteoforms in a high-throughput fashion. PMID:24023390

  13. BtcA, A class IA type III chaperone, interacts with the BteA N-terminal domain through a globular/non-globular mechanism.

    PubMed

    Guttman, Chen; Davidov, Geula; Yahalom, Adi; Shaked, Hadassa; Kolusheva, Sofiya; Bitton, Ronit; Barber-Zucker, Shiran; Chill, Jordan H; Zarivach, Raz

    2013-01-01

    Bordetella pertussis, the etiological agent of "whooping cough" disease, utilizes the type III secretion system (T3SS) to deliver a 69 kDa cytotoxic effector protein, BteA, directly into the host cells. As with other T3SS effectors, prior to its secretion BteA binds BtcA, a 13.9 kDa protein predicted to act as a T3SS class IA chaperone. While this interaction had been characterized for such effector-chaperone pairs in other pathogens, it has yet to be fully investigated in Bordetella. Here we provide the first biochemical proof that BtcA is indeed a class IA chaperone, responsible for the binding of BteA's N-terminal domain. We bring forth extensive evidence that BtcA binds its substrate effector through a dual-interface binding mechanism comprising of non-globular and bi-globular interactions at a moderate micromolar level binding affinity. We demonstrate that the non-globular interactions involve the first 31 N-terminal residues of BteA287 and their removal leads to destabilization of the effector-chaperone complex and lower binding affinities to BtcA. These findings represent an important first step towards a molecular understanding of BteA secretion and cell entry.

  14. Microtubules, Tubulins and Associated Proteins.

    ERIC Educational Resources Information Center

    Raxworthy, Michael J.

    1988-01-01

    Reviews much of what is known about microtubules, which are biopolymers consisting predominantly of subunits of the globular protein, tubulin. Describes the functions of microtubules, their structure and assembly, microtube associated proteins, and microtubule-disrupting agents. (TW)

  15. Understanding the Physical Properties that Control Protein Crystallization by Analysis of Large-Scale Experimental Data

    SciTech Connect

    Price, W.; Chen, Y; Handelman, S; Neely, H; Manor, P; Karlin, R; Nair, R; Montelione, G; Hunt, J; et. al.

    2008-01-01

    Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of entire predicted proteomes demonstrate substantial differences in the amino acid-sequence properties of human versus eubacterial proteins, which likely reflect differences in biophysical properties, including crystallization propensity. Our thermodynamic measurements do not generally support previous claims regarding correlations between sequence properties and protein stability.

  16. VARIABLES IN GLOBULAR CLUSTER NGC 5024

    SciTech Connect

    Safonova, M.; Stalin, C. S. E-mail: stalin@iiap.res.in

    2011-12-15

    We present the results of a commissioning campaign to observe Galactic globular clusters for the search of microlensing events. The central 10' Multiplication-Sign 10' region of the globular cluster NGC 5024 was monitored using the 2 m Himalayan Chandra Telescope in R-band for a period of about 8 hr on 2010 March 24. Light curves were obtained for nearly 10,000 stars using a modified Differential Image Analysis technique. We identified all known variables within our field of view and revised the periods and status of some previously reported short-period variables. We report about 70 new variable sources and present their equatorial coordinates, periods, light curves, and possible types. Out of these, 15 are SX Phe stars, 10 are W UMa-type stars, and 14 are probable RR Lyrae stars. Nine of the newly discovered SX Phe stars and one eclipsing binary belong to the blue straggler star population.

  17. The self-enrichment of globular clusters

    NASA Astrophysics Data System (ADS)

    Morgan, Siobahn; Lake, George

    1989-04-01

    It is shown that protoglobular clusters of primordial gas can confine the supernovae needed to enrich themselves. The required protocluster cloud masses and structural parameters are the same as those currently observed for the clusters. Two causal scenarios for star formation are examined to calculate the initial enrichment of primordial clouds. In the 'Christmas tree' scheme, the maximum final (Fe/H) is about 0.1. Since the time scale for formation and evolution of massive stars at the center of a cluster is nearly an order of magnitude less than the collapse time of the cluster, every globular cluster may have to survive a suprernova detonation. If this is the case, the minimum mass of a globular cluster is about 10 to the 4.6th solar mass.

  18. Detection of high-energy gamma-ray emission from the globular cluster 47 Tucanae with Fermi.

    PubMed

    Abdo, A A; Ackermann, M; Ajello, M; Atwood, W B; Axelsson, M; Baldini, L; Ballet, J; Barbiellini, G; Bastieri, D; Baughman, B M; Bechtol, K; Bellazzini, R; Berenji, B; Blandford, R D; Bloom, E D; Bonamente, E; Borgland, A W; Bregeon, J; Brez, A; Brigida, M; Bruel, P; Burnett, T H; Caliandro, G A; Cameron, R A; Caraveo, P A; Casandjian, J M; Cecchi, C; Celik, O; Charles, E; Chaty, S; Chekhtman, A; Cheung, C C; Chiang, J; Ciprini, S; Claus, R; Cohen-Tanugi, J; Conrad, J; Cutini, S; Dermer, C D; de Palma, F; Digel, S W; Dormody, M; do Couto e Silva, E; Drell, P S; Dubois, R; Dumora, D; Farnier, C; Favuzzi, C; Fegan, S J; Focke, W B; Frailis, M; Fukazawa, Y; Fusco, P; Gargano, F; Gasparrini, D; Gehrels, N; Germani, S; Giebels, B; Giglietto, N; Giordano, F; Glanzman, T; Godfrey, G; Grenier, I A; Grove, J E; Guillemot, L; Guiriec, S; Hanabata, Y; Harding, A K; Hayashida, M; Hays, E; Horan, D; Hughes, R E; Jóhannesson, G; Johnson, A S; Johnson, R P; Johnson, T J; Johnson, W N; Kamae, T; Katagiri, H; Kawai, N; Kerr, M; Knödlseder, J; Kuehn, F; Kuss, M; Lande, J; Latronico, L; Lemoine-Goumard, M; Longo, F; Loparco, F; Lott, B; Lovellette, M N; Lubrano, P; Makeev, A; Mazziotta, M N; McConville, W; McEnery, J E; Meurer, C; Michelson, P F; Mitthumsiri, W; Mizuno, T; Moiseev, A A; Monte, C; Monzani, M E; Morselli, A; Moskalenko, I V; Murgia, S; Nolan, P L; Norris, J P; Nuss, E; Ohsugi, T; Omodei, N; Orlando, E; Ormes, J F; Paneque, D; Panetta, J H; Parent, D; Pelassa, V; Pepe, M; Pierbattista, M; Piron, F; Porter, T A; Rainò, S; Rando, R; Razzano, M; Rea, N; Reimer, A; Reimer, O; Reposeur, T; Ritz, S; Rochester, L S; Rodriguez, A Y; Romani, R W; Roth, M; Ryde, F; Sadrozinski, H F-W; Sanchez, D; Sander, A; Saz Parkinson, P M; Sgrò, C; Smith, D A; Smith, P D; Spandre, G; Spinelli, P; Starck, J-L; Strickman, M S; Suson, D J; Tajima, H; Takahashi, H; Tanaka, T; Thayer, J B; Thayer, J G; Thompson, D J; Tibaldo, L; Torres, D F; Tosti, G; Tramacere, A; Uchiyama, Y; Usher, T L; Vasileiou, V; Vilchez, N; Vitale, V; Wang, P; Webb, N; Winer, B L; Wood, K S; Ylinen, T; Ziegler, M

    2009-08-14

    We report the detection of gamma-ray emissions above 200 megaelectron volts at a significance level of 17sigma from the globular cluster 47 Tucanae, using data obtained with the Large Area Telescope onboard the Fermi Gamma-ray Space Telescope. Globular clusters are expected to emit gamma rays because of the large populations of millisecond pulsars that they contain. The spectral shape of 47 Tucanae is consistent with gamma-ray emission from a population of millisecond pulsars. The observed gamma-ray luminosity implies an upper limit of 60 millisecond pulsars present in 47 Tucanae.

  19. APOGEE chemical abundances of globular cluster giants in the inner Galaxy

    NASA Astrophysics Data System (ADS)

    Schiavon, Ricardo P.; Johnson, Jennifer A.; Frinchaboy, Peter M.; Zasowski, Gail; Mészáros, Szabolcs; García-Hernández, D. A.; Cohen, Roger E.; Tang, Baitian; Villanova, Sandro; Geisler, Douglas; Beers, Timothy C.; Fernández-Trincado, J. G.; García Pérez, Ana E.; Lucatello, Sara; Majewski, Steven R.; Martell, Sarah L.; O'Connell, Robert W.; Prieto, Carlos Allende; Bizyaev, Dmitry; Carrera, Ricardo; Lane, Richard R.; Malanushenko, Elena; Malanushenko, Viktor; Muñoz, Ricardo R.; Nitschelm, Christian; Oravetz, Daniel; Pan, Kaike; Roman-Lopes, Alexandre; Schultheis, Matthias; Simmons, Audrey

    2017-04-01

    We report chemical abundances obtained by Sloan Digital Sky Survey (SDSS)-III/Apache Point Observatory Galactic Evolution Experiment for giant stars in five globular clusters located within 2.2 kpc of the Galactic Centre. We detect the presence of multiple stellar populations in four of those clusters (NGC 6553, NGC 6528, Terzan 5 and Palomar 6) and find strong evidence for their presence in NGC 6522. All clusters with a large enough sample present a significant spread in the abundances of N, C, Na and Al, with the usual correlations and anticorrelations between various abundances seen in other globular clusters. Our results provide important quantitative constraints on theoretical models for self-enrichment of globular clusters, by testing their predictions for the dependence of yields of elements such as Na, N, C and Al on metallicity. They also confirm that, under the assumption that field N-rich stars originate from globular cluster destruction, they can be used as tracers of their parental systems in the high-metallicity regime.

  20. THE OBSERVATIONAL AND THEORETICAL TIDAL RADII OF GLOBULAR CLUSTERS IN M87

    SciTech Connect

    Webb, Jeremy J.; Sills, Alison; Harris, William E.

    2012-02-10

    Globular clusters have linear sizes (tidal radii) which theory tells us are determined by their masses and by the gravitational potential of their host galaxy. To explore the relationship between observed and expected radii, we utilize the globular cluster population of the Virgo giant M87. Unusually deep, high signal-to-noise images of M87 are used to measure the effective and limiting radii of approximately 2000 globular clusters. To compare with these observations, we simulate a globular cluster population that has the same characteristics as the observed M87 cluster population. Placing these simulated clusters in the well-studied tidal field of M87, the orbit of each cluster is solved and the theoretical tidal radius of each cluster is determined. We compare the predicted relationship between cluster size and projected galactocentric distance to observations. We find that for an isotropic distribution of cluster velocities, theoretical tidal radii are approximately equal to observed limiting radii for R{sub gc} < 10 kpc. However, the isotropic simulation predicts a steep increase in cluster size at larger radii, which is not observed in large galaxies beyond the Milky Way. To minimize the discrepancy between theory and observations, we explore the effects of orbital anisotropy on cluster sizes, and suggest a possible orbital anisotropy profile for M87 which yields a better match between theory and observations. Finally, we suggest future studies which will establish a stronger link between theoretical tidal radii and observed radii.

  1. Potassium: A New Actor on the Globular Cluster Chemical Evolution Stage. The Case of NGC 2808

    NASA Astrophysics Data System (ADS)

    Mucciarelli, Alessio; Bellazzini, Michele; Merle, Thibault; Plez, Bertrand; Dalessandro, Emanuele; Ibata, Rodrigo

    2015-03-01

    We derive [K/Fe] abundance ratios for 119 stars in the globular cluster NGC 2808, all of them having O, Na, Mg, and Al abundances homogeneously measured in previous works. We detect an intrinsic star-to-star spread in the potassium abundance. Moreover [K/Fe] abundance ratios display statistically significant correlations with [Na/Fe] and [Al/Fe], and anti-correlations with [O/Fe] and [Mg/Fe]. All the four Mg deficient stars ([Mg/Fe] < 0.0) discovered so far in NGC 2808 are enriched in K by ~0.3 dex with respect to those with normal [Mg/Fe]. NGC 2808 is the second globular cluster, after NGC 2419, where a clear Mg-K anti-correlation is detected, albeit of weaker amplitude. The simultaneous correlation/anti-correlation of [K/Fe] with all the light elements usually involved in the chemical anomalies observed in globular cluster stars strongly support the idea that these abundance patterns are due to the same self-enrichment mechanism that produces Na-O and Mg-Al anti-correlations. This finding suggests that detectable spreads in K abundances may be typical in the massive globular clusters where the self-enrichment processes are observed to produce their most extreme manifestations. Based on data obtained at the ESO Very Large Telescope under the programs 072.D-0507 and 091.D-0329.

  2. Globular Clusters: Chemical Abundance - Integrated Colour calibration

    NASA Astrophysics Data System (ADS)

    Moyano Loyola, G.; Faifer, F. R.; Forte, J. C.

    In this work, we improve the chemical abundance - integrated colour cali- bration presented in Forte, Faifer & Geisler, 2007 (FFG07 hereafter) using a new (g-i) vs. (C-T1) colours calibration obtained from M87. Using this calibration and better values of the reddening for the galactic globulars, we found that a quadratic calibration is still enough to represent the observa- tional data, as in FFG07.

  3. Modelling the Milky Way's globular cluster system

    NASA Astrophysics Data System (ADS)

    Binney, James; Wong, Leong Khim

    2017-01-01

    We construct a model for the Galactic globular cluster system based on a realistic gravitational potential and a distribution function (DF) analytic in the action integrals. The DF comprises disc and halo components whose functional forms resemble those recently used to describe the stellar discs and stellar halo. We determine the posterior distribution of our model parameters using a Bayesian approach. This gives us an understanding of how well the globular cluster data constrain our model. The favoured parameter values of the disc and halo DFs are similar to values previously obtained from fits to the stellar disc and halo, although the cluster halo system shows clearer rotation than does the stellar halo. Our model reproduces the generic features of the globular cluster system, namely the density profile, the mean rotation velocity and the fraction of metal-rich clusters. However, the data indicate either incompatibility between catalogued cluster distances and current estimates of distance to the Galactic Centre, or failure to identify clusters behind the bulge. As the data for our Galaxy's components increase in volume and precision over the next few years, it will be rewarding to revisit the present analysis.

  4. Globular cluster formation - The fossil record

    NASA Technical Reports Server (NTRS)

    Murray, Stephen D.; Lin, Douglas N. C.

    1992-01-01

    Properties of globular clusters which have remained unchanged since their formation are used to infer the internal pressures, cooling times, and dynamical times of the protocluster clouds immediately prior to the onset of star formation. For all globular clusters examined, it is found that the cooling times are much less than the dynamical times, implying that the protoclusters must have been maintained in thermal equilibrium by external heat sources, with fluxes consistent with those found in previous work, and giving the observed rho-T relation. Self-gravitating clouds cannot be stably heated, so that the Jeans mass forms an upper limit to the cluster masses. The observed dependence of protocluster pressure upon galactocentric position implies that the protocluster clouds were in hydrostatic equilibrium after their formation. The pressure dependence is well fitted by that expected for a quasi-statically evolving background hot gas, shock heated to its virial temperature. The observations and inferences are combined with previous theoretical work to construct a picture of globular cluster formation.

  5. REGION OF GLOBULAR CLUSTER NGC 6397

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Right A NASA Hubble Space Telescope image of a small region (1.4 light-years across) in the globular star cluster NGC 6397 shows far fewer stars than would be expected in faint red dwarf stars were abundant. HST resolves about 200 stars. The stellar density is so low that HST can literally see right through the cluster and resolve far more distant background galaxies. This observation shows the surprising cutoff point below which nature apparently doesn't make many stars smaller that 1/5 the mass of our Sun. If there were lower mass stars in the cluster, then the image would contain an estimated 500 stars. This observation provides new insights into star formation in our Galaxy. Left A ground-based sky survey photograph of the globular cluster NGC 6397, one of the nearest and densest agglomerations of stars to Earth. The cluster is located 7,200 light-years away in the southern constellation Ara, and is one of 150 such objects which orbit our Milky Way Galaxy. Globular clusters are ideal laboratories for studying the formation and evolution of stars. This visible light picture was taken on March 3, 1994 with the Wide Field Planetary Camera 2, as part of the HST parallel observing program. Credit: F. Paresce, ST ScI and ESA and NASA

  6. STELLAR ENCOUNTER RATE IN GALACTIC GLOBULAR CLUSTERS

    SciTech Connect

    Bahramian, Arash; Heinke, Craig O.; Sivakoff, Gregory R.; Gladstone, Jeanette C.

    2013-04-01

    The high stellar densities in the cores of globular clusters cause significant stellar interactions. These stellar interactions can produce close binary mass-transferring systems involving compact objects and their progeny, such as X-ray binaries and radio millisecond pulsars. Comparing the numbers of these systems and interaction rates in different clusters drives our understanding of how cluster parameters affect the production of close binaries. In this paper we estimate stellar encounter rates ({Gamma}) for 124 Galactic globular clusters based on observational data as opposed to the methods previously employed, which assumed 'King-model' profiles for all clusters. By deprojecting cluster surface brightness profiles to estimate luminosity density profiles, we treat 'King-model' and 'core-collapsed' clusters in the same way. In addition, we use Monte Carlo simulations to investigate the effects of uncertainties in various observational parameters (distance, reddening, surface brightness) on {Gamma}, producing the first catalog of globular cluster stellar encounter rates with estimated errors. Comparing our results with published observations of likely products of stellar interactions (numbers of X-ray binaries, numbers of radio millisecond pulsars, and {gamma}-ray luminosity) we find both clear correlations and some differences with published results.

  7. Primordial black holes in globular clusters

    NASA Technical Reports Server (NTRS)

    Sigurdsson, Steinn; Hernquist, Lars

    1993-01-01

    It has recently been recognized that significant numbers of medium-mass back holes (of order 10 solar masses) should form in globular clusters during the early stages of their evolution. Here we explore the dynamical and observational consequences of the presence of such a primordial black-hole population in a globular cluster. The holes initially segregate to the cluster cores, where they form binary and multiple black-hole systems. The subsequent dynamical evolution of the black-hole population ejects most of the holes on a relatively short timescale: a typical cluster will retain between zero and four black holes in its core, and possibly a few black holes in its halo. The presence of binary, triple, and quadruple black-hole systems in cluster cores will disrupt main-sequence and giant stellar binaries; this may account for the observed anomalies in the distribution of binaries in globular clusters. Furthermore, tidal interactions between a multiple black-hole system and a red giant star can remove much of the red giant's stellar envelope, which may explain the puzzling absence of larger red giants in the cores of some very dense clusters.

  8. Crystal structure of zebrafish complement 1qA globular domain.

    PubMed

    Yuan, Hongyu; Chen, Rong; Tariq, Mansoor; Liu, Yanjie; Sun, Yaping; Xia, Chun

    2016-10-01

    C1q contains three globular domains (C1qgD) that are the key functional component of the classical complement system. C1qgD can interact with important immune molecules, including IgG and C-reactive protein (CRP) to form defense systems to protect animals. Here, the first non-mammalian structure, zebrafish C1qA globular domain (Dare-C1qAgD) was solved. Although the overall architecture of Dare-C1qAgD is similar to human C1qA, residues involved in C1qBgD, C1qCgD, and CRP binding are somewhat different while residues involved in IgG binding are not present in zebrafish. The structure gives insight into how human and fish C1qA evolved from an ancestral protein.

  9. Unfolding the Role of Large Heat Shock Proteins: New Insights and Therapeutic Implications

    PubMed Central

    Zuo, Daming; Subjeck, John; Wang, Xiang-Yang

    2016-01-01

    Heat shock proteins (HSPs) of eukaryotes are evolutionarily conserved molecules present in all the major intracellular organelles. They mainly function as molecular chaperones and participate in maintenance of protein homeostasis in physiological state and under stressful conditions. Despite their relative abundance, the large HSPs, i.e., Hsp110 and glucose-regulated protein 170 (Grp170), have received less attention compared to other conventional HSPs. These proteins are distantly related to the Hsp70 and belong to Hsp70 superfamily. Increased sizes of Hsp110 and Grp170, due to the presence of a loop structure, result in their exceptional capability in binding to polypeptide substrates or non-protein ligands, such as pathogen-associated molecules. These interactions that occur in the extracellular environment during tissue injury or microbial infection may lead to amplification of an immune response engaging both innate and adaptive immune components. Here, we review the current advances in understanding these large HSPs as molecular chaperones in proteostasis control and immune modulation as well as their therapeutic implications in treatment of cancer and neurodegeneration. Given their unique immunoregulatory activities, we also discuss the emerging evidence of their potential involvement in inflammatory and immune-related diseases. PMID:26973652

  10. Why protein R-factors are so large: a self-consistent analysis.

    PubMed

    Vitkup, Dennis; Ringe, Dagmar; Karplus, Martin; Petsko, Gregory A

    2002-03-01

    The R-factor and R-free are commonly used to measure the quality of protein models obtained in X-ray crystallography. Well-refined protein structures usually have R-factors in the range of 20-25%, whereas intrinsic errors in the experimental data are usually around 5%. We use molecular dynamics simulations to perform a self-consistent analysis by which we determine the major factors contributing to large values of protein R-factors. The analysis shows that significant R-factor values can arise from the use of isotropic B-factors to model anisotropic protein motions and from coordinate errors. Even in the absence of coordinate errors, the use of isotropic B-factors can cause the R-factors to be around 10%; for coordinate errors smaller than 0.2 A, the two errors types make similar contributions. The inaccuracy of the energy function used and multistate protein dynamics are unlikely to make significant contributions to the large R-factors.

  11. A Semiautomated Assignment Protocol for Methyl Group Side Chains in Large Proteins.

    PubMed

    Kim, Jonggul; Wang, Yingjie; Li, Geoffrey; Veglia, Gianluigi

    2016-01-01

    The developments of biosynthetic specific labeling strategies for side-chain methyl groups have allowed structural and dynamic characterization of very large proteins and protein complexes. However, the assignment of the methyl-group resonances remains an Achilles' heel for NMR, as the experiments designed to correlate side chains to the protein backbone become rather insensitive with the increase of the transverse relaxation rates. In this chapter, we outline a semiempirical approach to assign the resonances of methyl-group side chains in large proteins. This method requires a crystal structure or an NMR ensemble of conformers as an input, together with NMR data sets such as nuclear Overhauser effects (NOEs) and paramagnetic relaxation enhancements (PREs), to be implemented in a computational protocol that provides a probabilistic assignment of methyl-group resonances. As an example, we report the protocol used in our laboratory to assign the side chains of the 42-kDa catalytic subunit of the cAMP-dependent protein kinase A. Although we emphasize the labeling of isoleucine, leucine, and valine residues, this method is applicable to other methyl group side chains such as those of alanine, methionine, and threonine, as well as reductively methylated cysteine side chains.

  12. A Review of Methods Used for Identifying Structural Changes in a Large Protein Complex

    PubMed Central

    Nadeau, Owen W.; Carlson, Gerald M.

    2013-01-01

    This chapter explores the structural responses of a massive, hetero-oligomeric protein complex to a single allosteric activator as probed by a wide range of chemical, biochemical, and biophysical approaches. Some of the approaches used are amenable only to large protein targets, whereas others push the limits of their utility. Some of the techniques focus on individual subunits, or portions thereof, while others examine the complex as a whole. Despite the absence of crystallographic data for the complex, the diverse techniques identify and implicate a small region of its catalytic subunit as the master allosteric activation switch for the entire complex. PMID:22052488

  13. Accounting for large amplitude protein deformation during in silico macromolecular docking.

    PubMed

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

    Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  14. PPS, a large multidomain protein, functions with sex-lethal to regulate alternative splicing in Drosophila.

    PubMed

    Johnson, Matthew L; Nagengast, Alexis A; Salz, Helen K

    2010-03-05

    Alternative splicing controls the expression of many genes, including the Drosophila sex determination gene Sex-lethal (Sxl). Sxl expression is controlled via a negative regulatory mechanism where inclusion of the translation-terminating male exon is blocked in females. Previous studies have shown that the mechanism leading to exon skipping is autoregulatory and requires the SXL protein to antagonize exon inclusion by interacting with core spliceosomal proteins, including the U1 snRNP protein Sans-fille (SNF). In studies begun by screening for proteins that interact with SNF, we identified PPS, a previously uncharacterized protein, as a novel component of the machinery required for Sxl male exon skipping. PPS encodes a large protein with four signature motifs, PHD, BRK, TFS2M, and SPOC, typically found in proteins involved in transcription. We demonstrate that PPS has a direct role in Sxl male exon skipping by showing first that loss of function mutations have phenotypes indicative of Sxl misregulation and second that the PPS protein forms a complex with SXL and the unspliced Sxl RNA. In addition, we mapped the recruitment of PPS, SXL, and SNF along the Sxl gene using chromatin immunoprecipitation (ChIP), which revealed that, like many other splicing factors, these proteins bind their RNA targets while in close proximity to the DNA. Interestingly, while SNF and SXL are specifically recruited to their predicted binding sites, PPS has a distinct pattern of accumulation along the Sxl gene, associating with a region that includes, but is not limited to, the SxlPm promoter. Together, these data indicate that PPS is different from other splicing factors involved in male-exon skipping and suggest, for the first time, a functional link between transcription and SXL-mediated alternative splicing. Loss of zygotic PPS function, however, is lethal to both sexes, indicating that its role may be of broad significance.

  15. Understanding the Current Dynamical States of Globular Clusters

    NASA Astrophysics Data System (ADS)

    Pooley, David

    2008-09-01

    We appear to be on the verge of a major paradigm shift in our understanding of the current dynamical states of Galactic globular clusters. Fregeau (2008) brought together two recent theoretical breakthroughs as well as an observational breakthrough made possible by Chandra -- that a globular cluster's X-ray source population scales with its dynamical encounter frequency -- to persuasively argue that we have misunderstood the dynamical states of Galactic globular clusters. The observational evidence hinges on Chandra results from clusters which are classified as "core collapsed," of which there are only a handful of observations. I propose a nearly complete census with Chandra of the rest of the "core collapsed" globular clusters.

  16. Cosmic strings and the origin of globular clusters

    SciTech Connect

    Barton, Alistair; Brandenberger, Robert H.; Lin, Ling E-mail: rhb@physics.mcgill.ca

    2015-06-01

    We hypothesize that cosmic string loops are the seeds about which globular clusters accrete. Fixing the cosmic string tension by demanding that the peak in the distribution of masses of objects accreting onto string loops agrees with the peak in the observed mass distribution of globular clusters in our Milky Way galaxy, we then compute the expected number density and mass function of globular clusters, and compare with observations. Our hypothesis naturally explains why globular clusters are the oldest and most dense objects in a galaxy, and why they are found in the halo of the galaxy.

  17. RR Lyrae in Sagittarius Dwarf Globular Clusters (Poster abstract)

    NASA Astrophysics Data System (ADS)

    Pritzl, B. J.; Gehrman, T. J.; Bell, E.; Salinas, R.; Smith, H. A.; Catelan, M.

    2016-12-01

    (Abstract only) The Milky Way Galaxy was built up in part by the cannibalization of smaller dwarf galaxies. Some of them likely contained globular clusters. The Sagittarius dwarf galaxy provides a unique opportunity to study a system of globular clusters that originated outside the Milky Way. We have investigated the RR Lyrae populations in two Sagittarius globular clusters, Arp 2 and Terzan 8. The RR Lyrae are used to study the properties of the clusters and to compare this system to Milky Way globular clusters. We will discuss whether or not dwarf galaxies similar to the Sagittarius dwarf galaxy could have played a role in the formation of the Milky Way Galaxy.

  18. In search of massive single-population globular clusters

    NASA Astrophysics Data System (ADS)

    Caloi, Vittoria; D'Antona, Francesca

    2011-10-01

    The vast majority of globular clusters so far examined shows the chemical signatures of hosting (at least) two stellar populations. According to recent ideas, this feature requires a two-step process, in which the nuclearly processed matter from a 'first generation' (FG) of stars gives birth to a 'second generation' (SG), bearing the fingerprint of a fully carbon-nitrogen-oxygen (CNO) cycled matter. Since, as observed, the present population of most globular clusters is made up largely of SG stars, a substantial fraction of the FG (≳90 per cent) must be lost. Nevertheless, two types of clusters dominated by a simple stellar population (FG clusters) should exist: clusters initially too small to be able to retain a cooling flow and form a second generation (FG-only clusters) and massive clusters that could retain the CNO-processed ejecta and form an SG, but were unable to lose a significant fraction of their FG (mainly-FG clusters). Identification of mainly-FG clusters may provide an estimate of the fraction of the initial mass involved in the formation of the SG. We attempt a first classification of FG clusters, based on the morphology of their horizontal branches (HBs), as displayed in the published catalogues of photometric data for 106 clusters. We select, as FG candidates, the clusters in which the HB can be reproduced by the evolution of an almost unique mass. We find that less than 20 per cent of clusters with [Fe/H] < -0.8 appear to be FG, but only ˜10 per cent probably had a mass sufficient to form at all an SG. This small percentage confirms on a wider data base the spectroscopic result that the SG is a dominant constituent of today's clusters, suggesting that its formation is an ingredient necessary for the survival of globular clusters during their dynamical evolution in the Galactic tidal field. In more detail we show that Pal 3 turns out to be a good example of FG-only cluster. Instead, HB simulations and space distribution of its components indicate

  19. A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease.

    PubMed

    Tourette, Cendrine; Li, Biao; Bell, Russell; O'Hare, Shannon; Kaltenbach, Linda S; Mooney, Sean D; Hughes, Robert E

    2014-03-07

    Huntington disease (HD) is an inherited neurodegenerative disease caused by a CAG expansion in the HTT gene. Using yeast two-hybrid methods, we identified a large set of proteins that interact with huntingtin (HTT)-interacting proteins. This network, composed of HTT-interacting proteins (HIPs) and proteins interacting with these primary nodes, contains 3235 interactions among 2141 highly interconnected proteins. Analysis of functional annotations of these proteins indicates that primary and secondary HIPs are enriched in pathways implicated in HD, including mammalian target of rapamycin, Rho GTPase signaling, and oxidative stress response. To validate roles for HIPs in mutant HTT toxicity, we show that the Rho GTPase signaling components, BAIAP2, EZR, PIK3R1, PAK2, and RAC1, are modifiers of mutant HTT toxicity. We also demonstrate that Htt co-localizes with BAIAP2 in filopodia and that mutant HTT interferes with filopodial dynamics. These data indicate that HTT is involved directly in membrane dynamics, cell attachment, and motility. Furthermore, they implicate dysregulation in these pathways as pathological mechanisms in HD.

  20. SHRINKING THE BRANEWORLD: BLACK HOLE IN A GLOBULAR CLUSTER

    SciTech Connect

    Gnedin, Oleg Y.; Maccarone, Thomas J.; Psaltis, Dimitrios; Zepf, Stephen E. E-mail: tjm@astro.soton.ac.u E-mail: zepf@pa.msu.ed

    2009-11-10

    Large extra dimensions have been proposed as a possible solution to the hierarchy problem in physics. In one of the suggested models, the RS2 braneworld model, black holes may evaporate by Hawking radiation faster than in general relativity, on a timescale that depends on the black hole mass and on the asymptotic radius of curvature of the extra dimensions. Thus the size of the extra dimensions can be constrained by astrophysical observations. Here we point out that the black hole, recently discovered in an extragalactic globular cluster, places the strongest upper limit on the size of the extra dimensions in the RS2 model, L approx< 0.003 mm. This black hole has the virtues of old age and relatively small mass. The derived upper limit is within an order of magnitude of the absolute limit afforded by astrophysical observations of black holes.

  1. FAST ROTATING BLUE STRAGGLERS IN THE GLOBULAR CLUSTER M4

    SciTech Connect

    Lovisi, L.; Mucciarelli, A.; Ferraro, F. R.; Lanzoni, B.; Dalessandro, E.; Lucatello, S.; Gratton, R.; Beccari, G.; Rood, R. T.; Sills, A.; Fusi Pecci, F.; Piotto, G.

    2010-08-20

    We have used high-resolution spectra obtained with the spectrograph FLAMES at the European Southern Observatory Very Large Telescope to determine the kinematical properties and the abundance patterns of 20 blue straggler stars (BSSs) in the globular cluster (GC) M4. We found that {approx}40% of the measured BSSs are fast rotators (with rotational velocities >50 km s{sup -1}). This is the largest frequency of rapidly rotating BSSs ever detected in a GC. In addition, at odds with what has been found in 47 Tucanae, no evidence of carbon and/or oxygen depletion has been revealed in the sample of 11 BSSs for which we were able to measure the abundances. This could be due to either low statistics, or a different BSS formation process acting in M4.

  2. Globular cluster origin of X-ray bursters

    NASA Technical Reports Server (NTRS)

    Grindlay, J. E.

    1984-01-01

    X-ray bursters and galactic bulge X-ray sources, or the most luminous X-ray sources in the Galaxy, are reasonably well constrained in their basic nature but not in their origin. It is suggested they may all have been produced by tidal capture in high density cores of globular clusters, which have now largely been disrupted by tidal stripping and shocking in the galactic plane. General arguments are presented for cluster disruption by the possible ring of giant molecular clouds in the Galaxy. Tests of the cluster disruption hypothesis are in progress and preliminary results are summarized here. The G-K star 'companions' previously noted for at least four bursters have spectra (in the two cases observed) consistent with metal-rich cluster giants. Several possibilities are discussed, including the formation of hierarchical triples in the dissolving cluster or in the galactic plane.

  3. FORS2/VLT survey of Milky Way globular clusters. II. Fe and Mg abundances of 51 Milky Way globular clusters on a homogeneous scale

    NASA Astrophysics Data System (ADS)

    Dias, B.; Barbuy, B.; Saviane, I.; Held, E. V.; Da Costa, G. S.; Ortolani, S.; Gullieuszik, M.; Vásquez, S.

    2016-05-01

    Context. Globular clusters trace the formation and evolution of the Milky Way and surrounding galaxies, and outline their chemical enrichment history. To accomplish these tasks it is important to have large samples of clusters with homogeneous data and analysis to derive kinematics, chemical abundances, ages and locations. Aims: We obtain homogeneous metallicities and α-element enhancement for 51 Galactic bulge, disc, and halo globular clusters that are among the most distant and/or highly reddened in the Galaxy's globular cluster system. We also provide membership selection based on stellar radial velocities and atmospheric parameters. The implications of our results are discussed. Methods: We observed R ~ 2000 spectra in the wavelength interval 456-586 nm for over 800 red giant stars in 51 Galactic globular clusters. We applied full spectrum fitting with the code ETOILE together with libraries of observed and synthetic spectra. We compared the mean abundances of all clusters with previous work and with field stars. We used the relation between mean metallicity and horizontal branch morphology defined by all clusters to select outliers for discussion. Results: [Fe/H], [Mg/Fe], and [α/Fe] were derived in a consistent way for almost one-third of all Galactic globular clusters. We find our metallicities are comparable to those derived from high-resolution data to within σ = 0.08 dex over the interval -2.5< [Fe/H] < 0.0. Furthermore, a comparison of previous metallicity scales with our values yields σ< 0.16 dex. We also find that the distribution of [Mg/Fe] and [α/Fe] with [Fe/H] for the 51 clusters follows the general trend exhibited by field stars. It is the first time that the following clusters have been included in a large sample of homogeneous stellar spectroscopic observations and metallicity derivation: BH 176, Djorg 2, Pal 10, NGC 6426, Lynga 7, and Terzan 8. In particular, only photometric metallicities were available previously for the first three

  4. Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe.

    PubMed

    Necci, Marco; Piovesan, Damiano; Tosatto, Silvio C E

    2016-12-01

    Intrinsic disorder (ID) in proteins has been extensively described for the last decade; a large-scale classification of ID in proteins is mostly missing. Here, we provide an extensive analysis of ID in the protein universe on the UniProt database derived from sequence-based predictions in MobiDB. Almost half the sequences contain an ID region of at least five residues. About 9% of proteins have a long ID region of over 20 residues which are more abundant in Eukaryotic organisms and most frequently cover less than 20% of the sequence. A small subset of about 67,000 (out of over 80 million) proteins is fully disordered and mostly found in Viruses. Most proteins have only one ID, with short ID evenly distributed along the sequence and long ID overrepresented in the center. The charged residue composition of Das and Pappu was used to classify ID proteins by structural propensities and corresponding functional enrichment. Swollen Coils seem to be used mainly as structural components and in biosynthesis in both Prokaryotes and Eukaryotes. In Bacteria, they are confined in the nucleoid and in Viruses provide DNA binding function. Coils & Hairpins seem to be specialized in ribosome binding and methylation activities. Globules & Tadpoles bind antigens in Eukaryotes but are involved in killing other organisms and cytolysis in Bacteria. The Undefined class is used by Bacteria to bind toxic substances and mediate transport and movement between and within organisms in Viruses. Fully disordered proteins behave similarly, but are enriched for glycine residues and extracellular structures.

  5. Tafazzinsfrom Drosophila and Mammalian Cells Assemble in Large Protein Complexes with a Short Half-Life

    PubMed Central

    Xu, Yang; Malhotra, Ashim; Claypool, Steven M.; Ren, Mindong; Schlame, Michael

    2015-01-01

    Tafazzin is a transacylase that affects cardiolipin fatty acid composition and mitochondrial function. Mutations in human tafazzin cause Barth syndrome yet the enzyme has mostly been characterized in yeast. To study tafazzin in higher organisms, we isolated mitochondria from Drosophila and mammalian cell cultures. Our data indicate that tafazzin binds to multiple protein complexes in these organisms, and that the interactions of tafazzin lack strong specificity. Very large tafazzin complexes could only be detected in the presence of cardiolipin, but smaller complexes remained intact even upon treatment with phospholipase A2. In mammalian cells, tafazzin had a half-life of only 3–6 h, which was much shorter than the half-life of other mitochondrial proteins. The data suggest that tafazzin is a transient resident of multiple protein complexes. PMID:25598000

  6. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

    PubMed

    Kinjo, Akira R; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

    2017-01-04

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

  7. Direct detection of x-rays for protein crystallography employing a thick, large area CCD

    DOEpatents

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

    An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

  8. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

    PubMed Central

    Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

    2017-01-01

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. PMID:27789697

  9. Proteomics studies confirm the presence of alternative protein isoforms on a large scale

    PubMed Central

    Tress, Michael L; Bodenmiller, Bernd; Aebersold, Ruedi; Valencia, Alfonso

    2008-01-01

    Background Alternative splicing of messenger RNA permits the formation of a wide range of mature RNA transcripts and has the potential to generate a diverse spectrum of functional proteins. Although there is extensive evidence for large scale alternative splicing at the transcript level, there have been no comparable studies demonstrating the existence of alternatively spliced protein isoforms. Results Recent advances in proteomics technology have allowed us to carry out a comprehensive identification of protein isoforms in Drosophila. The analysis of this proteomic data confirmed the presence of multiple alternative gene products for over a hundred Drosophila genes. Conclusions We demonstrate that proteomics techniques can detect the expression of stable alternative splice isoforms on a genome-wide scale. Many of these alternative isoforms are likely to have regions that are disordered in solution, and specific proteomics methodologies may be required to identify these peptides. PMID:19017398

  10. cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.

    PubMed

    Pan, Yuchao; Dong, Yuxi; Zhou, Jingtian; Hallen, Mark; Donald, Bruce R; Zeng, Jianyang; Xu, Wei

    2016-09-01

    Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches.

  11. The Chemical Properties of Milky Way and M31 Globular Clusters. II. Stellar Population Model Predictions

    NASA Astrophysics Data System (ADS)

    Beasley, Michael A.; Brodie, Jean P.; Strader, Jay; Forbes, Duncan A.; Proctor, Robert N.; Barmby, Pauline; Huchra, John P.

    2005-03-01

    We derive ages, metallicities, and abundance ratios ([α/Fe]) from the integrated spectra of 23 globular clusters in M31 by employing multivariate fits to two different stellar population models. We also perform a parallel analysis on 21 Galactic globular clusters as a consistency check and in order to facilitate a differential analysis. Our analysis shows that the M31 globular clusters separate into three distinct components in age and metallicity; we identify an old, metal-poor group (seven clusters), an old, metal-rich group (10 clusters), and an intermediate-age (3-6 Gyr), intermediate-metallicity ([Z/H]~-1) group (six clusters). This third group is not identified in the Galactic globular cluster sample. We also see evidence that the old, metal-rich Galactic globular clusters are 1-2 Gyr older than their counterparts in M31. The majority of globular clusters in both samples appear to be enhanced in α-elements, but the degree of enhancement is rather model-dependent. The intermediate-age globular clusters appear to be the most enhanced, with [α/Fe]~0.4. These clusters are clearly depressed in CN with respect to the models and the bulk of the M31 and Milky Way sample. Compared with the bulge of M31, M32, and NGC 205, these clusters most resemble the stellar populations in NGC 205 in terms of age, metallicity, and CN abundance. We infer horizontal branch morphologies for the M31 clusters using the Rose Ca II index and demonstrate that blue horizontal branches are not leading to erroneous age estimates in our analysis. We discuss and reject as unlikely the hypothesis that these objects are in fact foreground stars contaminating the optical catalogs. The intermediate-age clusters have generally higher velocities than the bulk of the M31 cluster population. Spatially, three of these clusters are projected onto the bulge region, and the remaining three are distributed at large radii. We discuss these objects within the context of the build-up of the M31 halo and

  12. An Evolutionary View of the Arms Race between Protein Kinase R and Large DNA Viruses

    PubMed Central

    Carpentier, Kathryn S.

    2016-01-01

    To establish productive infections, viruses must counteract numerous cellular defenses that are poised to recognize viruses as nonself and to activate antiviral pathways. The opposing goals of host and viral factors lead to evolutionary arms races that can be illuminated by evolutionary and computational methods and tested in experimental models. Here we illustrate how this perspective has been contributing to our understanding of the interactions of the protein kinase R pathway with large DNA viruses. PMID:26792736

  13. A Complete Sample of Hot Post-AGB Stars in Globular Clusters

    NASA Technical Reports Server (NTRS)

    Landsman, W.; Moehler, S.; Napiwotzki, R.; Heber, U.; Sweigart, A.; Catelan, M.; Stecher, T.

    1999-01-01

    Ultraviolet images of globular clusters are often dominated by one or two "UV-bright" stars. The most luminous of these are believed to be post-AGB stars, which go through a luminous UV-bright phase as they leave the AGB and move rapidly across the HR diagram toward their final white dwarf state. During the two flights of the ASTRO observatory in 1990 and 1995, the Ultraviolet Imaging Telescope (UIT, Stecher 1997, PASP, 109, 584) was used to obtained ultraviolet (1600 A) images of 14 globular clusters. These images provide a complete census of hot (> 8000 K) post-AGB stars in the observed globular clusters, because the 40' field of view of UIT is large enough to image the entire population of most Galactic globulars, and because the dominant cool star population is suppressed in ultraviolet images, allowing UV-bright stars to be detected into the cluster core. We have begun a program of optical and STIS ultraviolet spectroscopy to determine the fundamental stellar parameters (\\log L, T_eff, \\log g) of all the hot post-AGB candidates discovered on the UIT images. Among the goals of our program are to test theoretical post-AGB lifetimes across the HR diagram, and to estimate the mass of the currently forming white dwarfs in globular clusters. Two trends are already apparent in our survey. First, the UV-selected sample has removed a bias against the detection of the hottest post-AGB stars, and resulted in the discovery of five cluster post-AGB stars with Teff > 50,000 K. Second, most of the new discoveries have been lower luminosity (2.5 $<$\\log L $<$ 3.0) than expected for stars which leave the AGB during the thermally pulsating phase.

  14. Resolving the timing problem of the globular clusters orbiting the Fornax dwarf galaxy

    NASA Astrophysics Data System (ADS)

    Angus, G. W.; Diaferio, A.

    2009-06-01

    We re-investigate the old problem of the survival of the five globular clusters (GCs) orbiting the Fornax dwarf galaxy in both standard and modified Newtonian dynamics (MOND). For the first time in the history of the topic, we use accurate mass models for the Fornax dwarf, obtained through Jeans modelling of the recently published line-of-sight (LOS) velocity dispersion data, and we are also not resigned to circular orbits for the GCs. Previously conceived problems stem from fixing the starting distances of the globulars to be less than half the tidal radius. We relax this constraint since there is absolutely no evidence for it and show that the dark matter (DM) paradigm, with either cusped or cored DM profiles, has no trouble sustaining the orbits of the two least massive GCs for a Hubble time almost regardless of their initial distance from Fornax. The three most massive globulars can remain in orbit as long as their starting distances are marginally outside the tidal radius. The outlook for MOND is also not nearly as bleak as previously reported. Although dynamical friction (DF) inside the tidal radius is far stronger in MOND, outside DF is negligible due to the absence of stars. This allows highly radial orbits to survive, but more importantly circular orbits at distances more than 85 per cent of Fornax's tidal radius to survive indefinitely. The probability of the GCs being on circular orbits at this distance compared with their current projected distances is discussed and shown to be plausible. Finally, if we ignore the presence of the most massive globular (giving it a large LOS distance), we demonstrate that the remaining four globulars can survive within the tidal radius for the Hubble time with perfectly sensible orbits.

  15. Large-scale serum protein biomarker discovery in Duchenne muscular dystrophy.

    PubMed

    Hathout, Yetrib; Brody, Edward; Clemens, Paula R; Cripe, Linda; DeLisle, Robert Kirk; Furlong, Pat; Gordish-Dressman, Heather; Hache, Lauren; Henricson, Erik; Hoffman, Eric P; Kobayashi, Yvonne Monique; Lorts, Angela; Mah, Jean K; McDonald, Craig; Mehler, Bob; Nelson, Sally; Nikrad, Malti; Singer, Britta; Steele, Fintan; Sterling, David; Sweeney, H Lee; Williams, Steve; Gold, Larry

    2015-06-09

    Serum biomarkers in Duchenne muscular dystrophy (DMD) may provide deeper insights into disease pathogenesis, suggest new therapeutic approaches, serve as acute read-outs of drug effects, and be useful as surrogate outcome measures to predict later clinical benefit. In this study a large-scale biomarker discovery was performed on serum samples from patients with DMD and age-matched healthy volunteers using a modified aptamer-based proteomics technology. Levels of 1,125 proteins were quantified in serum samples from two independent DMD cohorts: cohort 1 (The Parent Project Muscular Dystrophy-Cincinnati Children's Hospital Medical Center), 42 patients with DMD and 28 age-matched normal volunteers; and cohort 2 (The Cooperative International Neuromuscular Research Group, Duchenne Natural History Study), 51 patients with DMD and 17 age-matched normal volunteers. Forty-four proteins showed significant differences that were consistent in both cohorts when comparing DMD patients and healthy volunteers at a 1% false-discovery rate, a large number of significant protein changes for such a small study. These biomarkers can be classified by known cellular processes and by age-dependent changes in protein concentration. Our findings demonstrate both the utility of this unbiased biomarker discovery approach and suggest potential new diagnostic and therapeutic avenues for ameliorating the burden of DMD and, we hope, other rare and devastating diseases.

  16. Large-scale serum protein biomarker discovery in Duchenne muscular dystrophy

    PubMed Central

    Hathout, Yetrib; Brody, Edward; Clemens, Paula R.; Cripe, Linda; DeLisle, Robert Kirk; Furlong, Pat; Gordish-Dressman, Heather; Hache, Lauren; Henricson, Erik; Hoffman, Eric P.; Kobayashi, Yvonne Monique; Lorts, Angela; Mah, Jean K.; McDonald, Craig; Mehler, Bob; Nelson, Sally; Nikrad, Malti; Singer, Britta; Steele, Fintan; Sterling, David; Sweeney, H. Lee; Williams, Steve; Gold, Larry

    2015-01-01

    Serum biomarkers in Duchenne muscular dystrophy (DMD) may provide deeper insights into disease pathogenesis, suggest new therapeutic approaches, serve as acute read-outs of drug effects, and be useful as surrogate outcome measures to predict later clinical benefit. In this study a large-scale biomarker discovery was performed on serum samples from patients with DMD and age-matched healthy volunteers using a modified aptamer-based proteomics technology. Levels of 1,125 proteins were quantified in serum samples from two independent DMD cohorts: cohort 1 (The Parent Project Muscular Dystrophy–Cincinnati Children’s Hospital Medical Center), 42 patients with DMD and 28 age-matched normal volunteers; and cohort 2 (The Cooperative International Neuromuscular Research Group, Duchenne Natural History Study), 51 patients with DMD and 17 age-matched normal volunteers. Forty-four proteins showed significant differences that were consistent in both cohorts when comparing DMD patients and healthy volunteers at a 1% false-discovery rate, a large number of significant protein changes for such a small study. These biomarkers can be classified by known cellular processes and by age-dependent changes in protein concentration. Our findings demonstrate both the utility of this unbiased biomarker discovery approach and suggest potential new diagnostic and therapeutic avenues for ameliorating the burden of DMD and, we hope, other rare and devastating diseases. PMID:26039989

  17. Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit

    PubMed Central

    Petrov, Alexey N.; Meskauskas, Arturas; Roshwalb, Sara C.; Dinman, Jonathan D.

    2008-01-01

    Yeast ribosomal protein L10 (E. coli L16) is located at the center of a topological nexus that connects many functional regions of the large subunit. This essential protein has previously been implicated in processes as diverse as ribosome biogenesis, translational fidelity and mRNA stability. Here, the inability to maintain the yeast Killer virus was used as a proxy for large subunit defects to identify a series of L10 mutants. These mapped to roughly four discrete regions of the protein. A detailed analysis of mutants located in the N-terminal ‘hook’ of L10, which inserts into the bulge of 25S rRNA helix 89, revealed strong effects on rRNA structure corresponding to the entire path taken by the tRNA 3′ end as it moves through the large subunit during the elongation cycle. The mutant-induced structural changes are wide-ranging, affecting ribosome biogenesis, elongation factor binding, drug resistance/hypersensitivity, translational fidelity and virus maintenance. The importance of L10 as a potential transducer of information through the ribosome, and of a possible role of its N-terminal domain in switching between the pre- and post-translocational states are discussed. PMID:18824477

  18. Cortactin Adopts a Globular Conformation and Bundles Actin into Sheets

    SciTech Connect

    Cowieson, Nathan P.; King, Gordon; Cookson, David; Ross, Ian; Huber, Thomas; Hume, David A.; Kobe, Bostjan; Martin, Jennifer L.

    2008-08-21

    Cortactin is a filamentous actin-binding protein that plays a pivotal role in translating environmental signals into coordinated rearrangement of the cytoskeleton. The dynamic reorganization of actin in the cytoskeleton drives processes including changes in cell morphology, cell migration, and phagocytosis. In general, structural proteins of the cytoskeleton bind in the N-terminal region of cortactin and regulatory proteins in the C-terminal region. Previous structural studies have reported an extended conformation for cortactin. It is therefore unclear how cortactin facilitates cross-talk between structural proteins and their regulators. In the study presented here, circular dichroism, chemical cross-linking, and small angle x-ray scattering are used to demonstrate that cortactin adopts a globular conformation, thereby bringing distant parts of the molecule into close proximity. In addition, the actin bundling activity of cortactin is characterized, showing that fully polymerized actin filaments are bundled into sheet-like structures. We present a low resolution structure that suggests how the various domains of cortactin interact to coordinate its array of binding partners at sites of actin branching.

  19. Preparation and characterization of monodisperse large-porous silica microspheres as the matrix for protein separation.

    PubMed

    Xia, Hongjun; Wan, Guangping; Zhao, Junlong; Liu, Jiawei; Bai, Quan

    2016-11-04

    High performance liquid chromatography (HPLC) is a kind of efficient separation technology and has been used widely in many fields. Micro-sized porous silica microspheres as the most popular matrix have been used for fast separation and analysis in HPLC. In this paper, the monodisperse large-porous silica microspheres with controllable size and structure were successfully synthesized with polymer microspheres as the templates and characterized. First, the poly(glycidyl methacrylate-co-ethyleneglycol dimethacrylate) microspheres (PGMA-EDMA) were functionalized with tetraethylenepentamine (TEPA) to generate amino groups which act as a catalyst in hydrolysis of tetraethyl orthosilicate (TEOS) to form Si-containing low molecular weight species. Then the low molecular weight species diffused into the functionalized PGMA-EDMA microspheres by induction force of the amino groups to form polymer/silica hybrid microspheres. Finally, the organic polymer templates were removed by calcination, and the large-porous silica microspheres were obtained. The compositions, morphology, size distribution, specific surface area and pore size distribution of the porous silica microspheres were characterized by infrared analyzer, scanning-electron microscopy, dynamic laser scattering, the mercury intrusion method and thermal gravimetric analysis, respectively. The results show that the agglomeration of the hybrid microspheres can be overcome when the templates were functionalized with TEPA as amination reagent, and the yield of 95.7% of the monodisperse large-porous silica microspheres can be achieved with high concentration of polymer templates. The resulting large-porous silica microspheres were modified with octadecyltrichlorosilane (ODS) and the chromatographic evaluation was performed by separating the proteins and the digest of BSA. The baseline separation of seven kinds of protein standards was achieved, and the column delivered a better performance when separating BSA digests

  20. Breakthrough performance of large proteins on ion-exchange membrane columns.

    PubMed

    Montesinos-Cisneros, Rosa Maria; Lucero-Acuña, Armando; Ortega, Jaime; Guzmán, Roberto; Tejeda-Mansir, Armando

    2007-10-01

    Protein adsorption of large proteins on ion-exchange membrane columns was theoretically and experimentally investigated using batch and fixed-bed systems. Thyroglobulin was used as the model protein. The study strongly suggests that part of the protein is physically retained inside the column during frontal mode operation. These experimental results were used to obtain a filtration function of the chromatographic system. In the theoretical analysis of the frontal protein adsorption, a model was integrated by the serial coupling of the membrane-transport model, the filtration model and the system-dispersion model. Two different techniques were employed in the estimation of the maximum adsorption capacity, the equilibrium desorption constant and the forward interaction rate constant, which are the parameters of the membrane-transport model. The fit of the model to the experimental data was not possible using the equilibrium parameters obtained in the batch experiments. The parameter estimation using a simplex optimization routine coupled to the solution of the partial differential model equations yields full prediction of the adsorption phenomena.

  1. Live-cell multiphoton fluorescence correlation spectroscopy with an improved large Stokes shift fluorescent protein

    PubMed Central

    Guan, Yinghua; Meurer, Matthias; Raghavan, Sarada; Rebane, Aleksander; Lindquist, Jake R.; Santos, Sofia; Kats, Ilia; Davidson, Michael W.; Mazitschek, Ralph; Hughes, Thomas E.; Drobizhev, Mikhail; Knop, Michael; Shah, Jagesh V.

    2015-01-01

    We report an improved variant of mKeima, a monomeric long Stokes shift red fluorescent protein, hmKeima8.5. The increased intracellular brightness and large Stokes shift (∼180 nm) make it an excellent partner with teal fluorescent protein (mTFP1) for multiphoton, multicolor applications. Excitation of this pair by a single multiphoton excitation wavelength (MPE, 850 nm) yields well-separable emission peaks (∼120-nm separation). Using this pair, we measure homo- and hetero-oligomerization interactions in living cells via multiphoton excitation fluorescence correlation spectroscopy (MPE-FCS). Using tandem dimer proteins and small-molecule inducible dimerization domains, we demonstrate robust and quantitative detection of intracellular protein–protein interactions. We also use MPE-FCCS to detect drug–protein interactions in the intracellular environment using a Coumarin 343 (C343)-conjugated drug and hmKeima8.5 as a fluorescence pair. The mTFP1/hmKeima8.5 and C343/hmKeima8.5 combinations, together with our calibration constructs, provide a practical and broadly applicable toolbox for the investigation of molecular interactions in the cytoplasm of living cells. PMID:25877871

  2. Effect of initial microstructure on plastic flow and dynamic globularization during hot working of Ti-6Al-4V

    SciTech Connect

    Shell, E.B.; Semiatin, S.L.

    1999-12-01

    Plastic flow behavior and globularization kinetics during subtransus hot working were determined for Ti-6Al-4V with three different transformed beta microstructures. These conditions consisted of fine lamellar colonies, a mixture of coarse colonies and acicular alpha, and acicular alpha. Isothermal hot compression tests were performed on cylindrical samples at subtransus temperatures and strain rates typical of ingot breakdown (i.e., T {approximately} 815 C to 955 C, {bar {epsilon}} {approximately} 0.1 s{sup {minus}1}). For all three material conditions, true stress-true strain curves exhibited a peak stress followed by noticeable flow softening; the values of peak stress and flow softening rate showed little dependence on starting microstructure. On the other hand, the kinetics of dynamic globularization varied noticeably with microstructure. By and large, the globularization rate under a given set of deformation conditions was most rapid for the fine acicular microstructure and least rapid for the mixed coarse-colony/acicular structure. At temperatures close to the beta transus, however, the difference in globularization rates for the three microstructures was less, an effect attributed to the rapid (continuous) coarsening of the laths in the acicular microstructure during preheating prior to hot working. The absence of a correlation between the globularization kinetics and the observed flow softening at low strains suggested platelet/lath bending and kinking as the primary deformation mechanism that controls the shape of the flow curves.

  3. Rice Ribosomal Protein Large Subunit Genes and Their Spatio-temporal and Stress Regulation

    PubMed Central

    Moin, Mazahar; Bakshi, Achala; Saha, Anusree; Dutta, Mouboni; Madhav, Sheshu M.; Kirti, P. B.

    2016-01-01

    Ribosomal proteins (RPs) are well-known for their role in mediating protein synthesis and maintaining the stability of the ribosomal complex, which includes small and large subunits. In the present investigation, in a genome-wide survey, we predicted that the large subunit of rice ribosomes is encoded by at least 123 genes including individual gene copies, distributed throughout the 12 chromosomes. We selected 34 candidate genes, each having 2–3 identical copies, for a detailed characterization of their gene structures, protein properties, cis-regulatory elements and comprehensive expression analysis. RPL proteins appear to be involved in interactions with other RP and non-RP proteins and their encoded RNAs have a higher content of alpha-helices in their predicted secondary structures. The majority of RPs have binding sites for metal and non-metal ligands. Native expression profiling of 34 ribosomal protein large (RPL) subunit genes in tissues covering the major stages of rice growth shows that they are predominantly expressed in vegetative tissues and seedlings followed by meiotically active tissues like flowers. The putative promoter regions of these genes also carry cis-elements that respond specifically to stress and signaling molecules. All the 34 genes responded differentially to the abiotic stress treatments. Phytohormone and cold treatments induced significant up-regulation of several RPL genes, while heat and H2O2 treatments down-regulated a majority of them. Furthermore, infection with a bacterial pathogen, Xanthomonas oryzae, which causes leaf blight also induced the expression of 80% of the RPL genes in leaves. Although the expression of RPL genes was detected in all the tissues studied, they are highly responsive to stress and signaling molecules indicating that their encoded proteins appear to have roles in stress amelioration besides house-keeping. This shows that the RPL gene family is a valuable resource for manipulation of stress tolerance in

  4. Chemical abundances in the old LMC globular cluster Hodge 11

    NASA Astrophysics Data System (ADS)

    Mateluna, R.; Geisler, D.; Villanova, S.; Carraro, G.; Grocholski, A.; Sarajedini, A.; Cole, A.; Smith, V.

    2012-12-01

    Context. The study of globular clusters is one of the most powerful ways to learn about a galaxy's chemical evolution and star formation history. They preserve a record of chemical abundances at the time of their formation and are relatively easy to age date. The most detailed knowledge of the chemistry of a star is given by high resolution spectroscopy, which provides accurate abundances for a wide variety of elements, yielding a wealth of information on the various processes involved in the cluster's chemical evolution. Aims: We studied red giant branch (RGB) stars in an old, metal-poor globular cluster of the Large Magellanic Cloud (LMC), Hodge 11 (H11), in order to measure as many elements as possible. The goal is to compare its chemical trends to those in the Milky Way halo and dwarf spheroidal galaxies in order to help understand the formation history of the LMC and our own Galaxy. Methods: We have obtained high resolution VLT/FLAMES spectra of eight RGB stars in H11. The spectral range allowed us to measure a variety of elements, including Fe, Mg, Ca, Ti, Si, Na, O, Ni, Cr, Sc, Mn, Co, Zn, Ba, La, Eu and Y. Results: We derived a mean [Fe/H] = -2.00 ± 0.04, in the middle of previous determinations. We found low [α/Fe] abundances for our targets, more comparable to values found in dwarf spheroidal galaxies than in the Galactic halo, suggesting that if H11 is representative of its ancient populations then the LMC does not represent a good halo building block. Our [Ca/Fe] value is about 0.3 dex less than that of halo stars used to calibrate the Ca IR triplet technique for deriving metallicity. A hint of a Na abundance spread is observed. Its stars lie at the extreme high O, low Na end of the Na:O anti-correlation displayed by Galactic and LMC globular clusters. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile (proposal ID 082.B-0458).Table 4 is only available in electronic form at http://www.aanda.org

  5. Isolated elliptical galaxies and their globular cluster systems. II. NGC 7796 - globular clusters, dynamics, companion

    NASA Astrophysics Data System (ADS)

    Richtler, T.; Salinas, R.; Lane, R. R.; Hilker, M.; Schirmer, M.

    2015-02-01

    Context. Rich globular cluster systems, particularly the metal-poor part of them, are thought to be the visible manifestations of long-term accretion processes. The invisible part is the dark matter halo, which may show some correspondence to the globular cluster system. It is therefore interesting to investigate the globular cluster systems of isolated elliptical galaxies, which supposedly have not experienced extended accretion. Aims: We investigate the globular cluster system of the isolated elliptical NGC 7796, present new photometry of the galaxy, and use published kinematical data to constrain the dark matter content. Methods: Deep images in B and R, obtained with the VIsible MultiObject Spectrograph (VIMOS) at the VLT, form the data base. We performed photometry with DAOPHOT and constructed a spherical photometric model. We present isotropic and anisotropic Jeans-models and give a morphological description of the companion dwarf galaxy. Results: The globular cluster system has about 2000 members, so it is not as rich as those of giant ellipticals in galaxy clusters with a comparable stellar mass, but richer than many cluster systems of other isolated ellipticals. The colour distribution of globular clusters is bimodal, which does not necessarily mean a metallicity bimodality. The kinematic literature data are somewhat inconclusive. The velocity dispersion in the inner parts can be reproduced without dark matter under isotropy. Radially anisotropic models need a low stellar mass-to-light ratio, which would contrast with the old age of the galaxy. A MONDian model is supported by X-ray analysis and previous dynamical modelling, but better data are necessary for a confirmation. The dwarf companion galaxy NGC 7796-1 exhibits tidal tails, multiple nuclei, and very boxy isophotes. Conclusions: NGC 7796 is an old, massive isolated elliptical galaxy with no indications of later major star formation events as seen frequently in other isolated ellipticals. Its

  6. Bacillus thuringiensis Cyt2Aa2 toxin disrupts cell membranes by forming large protein aggregates

    PubMed Central

    Tharad, Sudarat; Toca-Herrera, José L.; Promdonkoy, Boonhiang; Krittanai, Chartchai

    2016-01-01

    Bacillus thuringiensis (Bt) Cyt2Aa2 showed toxicity against Dipteran insect larvae and in vitro lysis activity on several cells. It has potential applications in the biological control of insect larvae. Although pore-forming and/or detergent-like mechanisms were proposed, the mechanism underlying cytolytic activity remains unclear. Analysis of the haemolytic activity of Cyt2Aa2 with osmotic stabilizers revealed partial toxin inhibition, suggesting a distinctive mechanism from the putative pore formation model. Membrane permeability was studied using fluorescent dye entrapped in large unilamellar vesicles (LUVs) at various protein/lipid molar ratios. Binding of Cyt2Aa2 monomer to the lipid membrane did not disturb membrane integrity until the critical protein/lipid molar ratio was reached, when Cyt2Aa2 complexes and cytolytic activity were detected. The complexes are large aggregates that appeared as a ladder when separated by agarose gel electrophoresis. Interaction of Cyt2Aa2 with Aedes albopictus cells was investigated by confocal microscopy and total internal reflection fluorescent microscopy (TIRF). The results showed that Cyt2Aa2 binds on the cell membrane at an early stage without cell membrane disruption. Protein aggregation on the cell membrane was detected later which coincided with cell swelling. Cyt2Aa2 aggregations on supported lipid bilayers (SLBs) were visualized by AFM. The AFM topographic images revealed Cyt2Aa2 aggregates on the lipid bilayer at low protein concentration and subsequently disrupts the lipid bilayer by forming a lesion as the protein concentration increased. These results supported the mechanism whereby Cyt2Aa2 binds and aggregates on the lipid membrane leading to the formation of non-specific hole and disruption of the cell membrane. PMID:27612497

  7. THE PRODUCTION RATE OF SN Ia EVENTS IN GLOBULAR CLUSTERS

    SciTech Connect

    Washabaugh, Pearce C.; Bregman, Joel N. E-mail: jbregman@umich.edu

    2013-01-01

    In globular clusters, dynamical evolution produces luminous X-ray emitting binaries at a rate about 200 times greater than in the field. If globular clusters also produce SN Ia at a high rate, it would account for many of the SN Ia production in early-type galaxies and provide insight into their formation. Here we use archival Hubble Space Telescope (HST) images of nearby galaxies that have hosted an SN Ia to examine the rate at which globular clusters produce these events. The location of the SN Ia is registered on an HST image obtained before the event or after the supernova (SN) faded. Of the 36 nearby galaxies examined, 21 had sufficiently good data to search for globular cluster hosts. None of the 21 SNe have a definite globular cluster counterpart, although there are some ambiguous cases. This places an upper limit to the enhancement rate of SN Ia production in globular clusters of about 42 at the 95% confidence level, which is an order of magnitude lower than the enhancement rate for luminous X-ray binaries. Even if all of the ambiguous cases are considered as having a globular cluster counterpart, the upper bound for the enhancement rate is 82 at the 95% confidence level, still a factor of several below that needed to account for half of the SN Ia events. Barring unforeseen selection effects, we conclude that globular clusters are not responsible for producing a significant fraction of the SN Ia events in early-type galaxies.

  8. Globular glial tauopathies (GGT): consensus recommendations.

    PubMed

    Ahmed, Zeshan; Bigio, Eileen H; Budka, Herbert; Dickson, Dennis W; Ferrer, Isidro; Ghetti, Bernardino; Giaccone, Giorgio; Hatanpaa, Kimmo J; Holton, Janice L; Josephs, Keith A; Powers, James; Spina, Salvatore; Takahashi, Hitoshi; White, Charles L; Revesz, Tamas; Kovacs, Gabor G

    2013-10-01

    Recent studies have highlighted a group of 4-repeat (4R) tauopathies that are characterised neuropathologically by widespread, globular glial inclusions (GGIs). Tau immunohistochemistry reveals 4R immunoreactive globular oligodendroglial and astrocytic inclusions and the latter are predominantly negative for Gallyas silver staining. These cases are associated with a range of clinical presentations, which correlate with the severity and distribution of underlying tau pathology and neurodegeneration. Their heterogeneous clinicopathological features combined with their rarity and under-recognition have led to cases characterised by GGIs being described in the literature using various and redundant terminologies. In this report, a group of neuropathologists form a consensus on the terminology and classification of cases with GGIs. After studying microscopic images from previously reported cases with suspected GGIs (n = 22), this panel of neuropathologists with extensive experience in the diagnosis of neurodegenerative diseases and a documented record of previous experience with at least one case with GGIs, agreed that (1) GGIs were present in all the cases reviewed; (2) the morphology of globular astrocytic inclusions was different to tufted astrocytes and finally that (3) the cases represented a number of different neuropathological subtypes. They also agreed that the different morphological subtypes are likely to be part of a spectrum of a distinct disease entity, for which they recommend that the overarching term globular glial tauopathy (GGT) should be used. Type I cases typically present with frontotemporal dementia, which correlates with the fronto-temporal distribution of pathology. Type II cases are characterised by pyramidal features reflecting motor cortex involvement and corticospinal tract degeneration. Type III cases can present with a combination of frontotemporal dementia and motor neuron disease with fronto-temporal cortex, motor cortex and

  9. Dynamics of the globular cluster NGC 362

    NASA Technical Reports Server (NTRS)

    Fischer, Philippe; Welch, Douglas L.; Mateo, Mario; Cote, Patrick

    1993-01-01

    A combination of V-band CCD images and echelle spectra of member red giants is presently used to examine the internal dynamics of the globular cluster NGC 362. A total of 285 stellar spectra were obtained of 215 stars for radial velocity determinations, and the true cluster binary fraction was determined from simulations to be 0.15 for circular orbits and 0.27 for orbits with an f(e) = e (eccentricity) distribution function. An overabundance of binaries is surmised for NGC 362 on this basis.

  10. HUBBLE PINPOINTS WHITE DWARFS IN GLOBULAR CLUSTER

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Peering deep inside a cluster of several hundred thousand stars, NASA's Hubble Space Telescope uncovered the oldest burned-out stars in our Milky Way Galaxy. Located in the globular cluster M4, these small, dying stars - called white dwarfs - are giving astronomers a fresh reading on one of the biggest questions in astronomy: How old is the universe? The ancient white dwarfs in M4 are about 12 to 13 billion years old. After accounting for the time it took the cluster to form after the big bang, astronomers found that the age of the white dwarfs agrees with previous estimates for the universe's age. In the top panel, a ground-based observatory snapped a panoramic view of the entire cluster, which contains several hundred thousand stars within a volume of 10 to 30 light-years across. The Kitt Peak National Observatory's 0.9-meter telescope took this picture in March 1995. The box at left indicates the region observed by the Hubble telescope. The Hubble telescope studied a small region of the cluster. A section of that region is seen in the picture at bottom left. A sampling of an even smaller region is shown at bottom right. This region is only about one light-year across. In this smaller region, Hubble pinpointed a number of faint white dwarfs. The blue circles pinpoint the dwarfs. It took nearly eight days of exposure time over a 67-day period to find these extremely faint stars. Globular clusters are among the oldest clusters of stars in the universe. The faintest and coolest white dwarfs within globular clusters can yield a globular cluster's age. Earlier Hubble observations showed that the first stars formed less than 1 billion years after the universe's birth in the big bang. So, finding the oldest stars puts astronomers within arm's reach of the universe's age. M4 is 7,000 light-years away in the constellation Scorpius. Hubble's Wide Field and Planetary Camera 2 made the observations from January through April 2001. These optical observations were combined to

  11. UV Spectroscopic Indices of Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Morales-Hernández, J.; Chávez, M.; Bertone, E.; Buzzoni, A.; Bressan, A.

    2009-03-01

    We present the calculation of a set of 12 mid-ultraviolet (1900-3200 Å) spectroscopic indices for a sample of 15 galactic globular clusters (GGC) observed with the International Ultraviolet Explorer (IUE). We explore the dependence of the indices on age and metal abundance. We found that five indices (BL 2538, Fe II 2609, Mg II 2800, Mg I 2852 and Mg Wide) display a remarkably good correlation with [Fe/H]. With respect to age, only one index (BL 2740) shows a good correlation. Results from theoretical simple stellar populations well reproduce the global trends of indices vs. [Fe/H].

  12. Globular glial tauopathies (GGT): consensus recommendations

    PubMed Central

    Bigio, Eileen H.; Budka, Herbert; Dickson, Dennis W.; Ferrer, Isidro; Ghetti, Bernardino; Giaccone, Giorgio; Hatanpaa, Kimmo J.; Holton, Janice L.; Josephs, Keith A.; Powers, James; Spina, Salvatore; Takahashi, Hitoshi; White, Charles L.; Revesz, Tamas

    2014-01-01

    Rrecent studies have highlighted a group of 4-repeat (4R) tauopathies that are characterised neuropathologically by widespread, globular glial inclusions (GGIs). Tau immunohistochemistry reveals 4R immunore-active globular oligodendroglial and astrocytic inclusions and the latter are predominantly negative for Gallyas silver staining. These cases are associated with a range of clinical presentations, which correlate with the severity and distribution of underlying tau pathology and neurodegeneration. Their heterogeneous clinicopathological features combined with their rarity and under-recognition have led to cases characterised by GGIs being described in the literature using various and redundant terminologies. In this report, a group of neuropathologists form a consensus on the terminology and classification of cases with GGIs. After studying microscopic images from previously reported cases with suspected GGIs (n = 22), this panel of neuropathologists with extensive experience in the diagnosis of neurodegenerative diseases and a documented record of previous experience with at least one case with GGIs, agreed that (1) GGIs were present in all the cases reviewed; (2) the morphology of globular astrocytic inclusions was different to tufted astrocytes and finally that (3) the cases represented a number of different neuropathological subtypes. They also agreed that the different morphological subtypes are likely to be part of a spectrum of a distinct disease entity, for which they recommend that the overarching term globular glial tauopathy (GGT) should be used. Type I cases typically present with frontotemporal dementia, which correlates with the fronto-temporal distribution of pathology. Type II cases are characterised by pyramidal features reflecting motor cortex involvement and corticospinal tract degeneration. Type III cases can present with a combination of frontotemporal dementia and motor neuron disease with fronto-temporal cortex, motor cortex and

  13. The Dynamics Of Galactic Globular Cluster

    NASA Astrophysics Data System (ADS)

    Ding, Chen

    2008-10-01

    We have used the Hubble Space Telescope (HST) to measure proper motion of the globular cluster NGC 6656 (M22) with respect to the background bulge stars and its internal velocity dispersion profile. With the space velocity of (Π, Θ, W) = (184±3, 209±14, 132±15) km s-1, we also calculate the orbit of the cluster. The central velocity dispersion in both components of the proper motion of cluster stars is 16.99 km s-1. We derive the mass-to-ration (M/L)˜1.7 which is relatively higher than the past works.

  14. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes

    NASA Astrophysics Data System (ADS)

    Lu, Jonathan; Trnka, Michael J.; Roh, Soung-Hun; Robinson, Philip J. J.; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L.; Guan, Shenheng

    2015-12-01

    Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise.

  15. Dynamical friction in multi-component evolving globular clusters

    SciTech Connect

    Alessandrini, Emiliano; Lanzoni, Barbara; Miocchi, Paolo; Ciotti, Luca; Ferraro, Francesco R.

    2014-11-10

    We use the Chandrasekhar formalism and direct N-body simulations to study the effect of dynamical friction on a test object only slightly more massive than the field stars, orbiting a spherically symmetric background of particles with a mass spectrum. The main goal is to verify whether the dynamical friction time (t {sub DF}) develops a non-monotonic radial dependence that could explain the bimodality of the blue straggler radial distributions observed in globular clusters. In these systems, in fact, relaxation effects lead to a mass and velocity radial segregation of the different mass components, so that mass-spectrum effects on t {sub DF} are expected to be dependent on radius. We find that in spite of the presence of different masses, t {sub DF} is always a monotonic function of radius, at all evolutionary times and independently of the initial concentration of the simulated cluster. This is because the radial dependence of t {sub DF} is largely dominated by the total mass density profile of the background stars (which is monotonically decreasing with radius). Hence, a progressive temporal erosion of the blue straggler star (BSS) population at larger and larger distances from the cluster center remains the simplest and the most likely explanation of the shape of the observed BSS radial distributions, as suggested in previous works. We also confirm the theoretical expectation that approximating a multi-mass globular cluster as made of (averaged) equal-mass stars can lead to significant overestimations of t {sub DF} within the half-mass radius.

  16. Study of Diffuse X-ray Emission in Globular Clusters

    NASA Technical Reports Server (NTRS)

    Grindlay, Jonathan E.

    1997-01-01

    This grant supported our analysis of ROSAT x-ray data on globular clusters. Although the grant title referred to our original ROSAT proposal (cycle 1) to study diffuse soft x-ray emission in three globulars (for which time was only granted in that original observing cycle for one cluster, 47 Tuc), the grant has also been maintained through several renewals and funding supplements to support our later ROSAT observations of point sources in globulars. The primary emphasis has been on the study of the dim sources, or low liuminosity globular cluster x-ray sources, which we had originally discovered with the Einstein Observatory and for which ROSAT provided the logical followup. In this Final Report, we summarize the Scientific Objectives of this investigation of both diffuse emission and dim sources in globular clusters and the Results Achieved; and finally the Papers Published.

  17. Large scale crystallization of protein pharmaceuticals in microgravity via temperature change

    NASA Technical Reports Server (NTRS)

    Long, Marianna M.

    1992-01-01

    The major objective of this research effort is the temperature driven growth of protein crystals in large batches in the microgravity environment of space. Pharmaceutical houses are developing protein products for patient care, for example, human insulin, human growth hormone, interferons, and tissue plasminogen activator or TPA, the clot buster for heart attack victims. Except for insulin, these are very high value products; they are extremely potent in small quantities and have a great value per gram of material. It is feasible that microgravity crystallization can be a cost recoverable, economically sound final processing step in their manufacture. Large scale protein crystal growth in microgravity has significant advantages from the basic science and the applied science standpoints. Crystal growth can proceed unhindered due to lack of surface effects. Dynamic control is possible and relatively easy. The method has the potential to yield large quantities of pure crystalline product. Crystallization is a time honored procedure for purifying organic materials and microgravity crystallization could be the final step to remove trace impurities from high value protein pharmaceuticals. In addition, microgravity grown crystals could be the final formulation for those medicines that need to be administered in a timed release fashion. Long lasting insulin, insulin lente, is such a product. Also crystalline protein pharmaceuticals are more stable for long-term storage. Temperature, as the initiation step, has certain advantages. Again, dynamic control of the crystallization process is possible and easy. A temperature step is non-invasive and is the most subtle way to control protein solubility and therefore crystallization. Seeding is not necessary. Changes in protein and precipitant concentrations and pH are not necessary. Finally, this method represents a new way to crystallize proteins in space that takes advantage of the unique microgravity environment. The results

  18. Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

    SciTech Connect

    Galat, Andrzej Thai, Robert

    2014-08-08

    Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

  19. Calculation of subunit stoichiometry of large, multisubunit proteins from amino acid compositions.

    PubMed

    Kapp, O H; Qabar, A N; Vinogradov, S N

    1990-01-01

    The subunit stoichiometry of a large, multisubunit protein can be determined from the molar amino acid compositions (i amino acids) of the protein and its subunits. The number of copies of the subunits (1, 2, ... j) is calculated by solving all possible combinations of simultaneous equations in j unknowns (i!/j!(i - j)!). Calculations carried out using the published amino acid compositions determined by analysis and the compositions calculated from the sequences for two proteins of known stoichiometry provided the following results: Escherichia coli aspartate transcarbamoylase (R6C6, Mr = 307.5 kDa), R = 5.6 to 6.6 and C = 5.8 to 6.3, and spinach ribulose-bisphosphate carboxylase (L8S8, Mr = 535 kDa), L = 7.3 to 9.1 and S = 5.6 to 10.6. Calculations were also carried out with the amino acid compositions of two much larger proteins, the E. coli pyruvate dehydrogenase complex, Mr = 5280 kDa, subunits E1 (99.5 kDa), E2 (66 kDa), and E3 (50.6 kDa), and the extracellular hemoglobin of Lumbricus terrestris, Mr = 3760 kDa, subunits M (17 kDa), D1 (31 kDa), D2 (37 kDa), and T (51 kDa); the results for PDHase were E1 = 20 to 24, E2 = 18 to 31, E3 = 21 to 33 and those for Lumbricus hemoglobin were M = 34 to 46, D1 = 13 to 19, D2 = 13 to 18, and T = 34 to 36. Although the sample standard deviations of the mean values are generally high, the proposed method works surprisingly well for the two smaller proteins and provides physically reasonable results for the two larger proteins.

  20. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex

    PubMed Central

    Lyumkis, Dmitry; Oliveira dos Passos, Dario; Tahara, Erich B.; Webb, Kristofor; Bennett, Eric J.; Vinterbo, Staal; Potter, Clinton S.; Carragher, Bridget; Joazeiro, Claudio A. P.

    2014-01-01

    All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), composed of the listerin/Ltn1 E3 ubiquitin ligase and cofactors, mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. How RQC recognizes stalled ribosomes and performs its functions has not been understood. Using single-particle cryoelectron microscopy, we have determined the structure of the RQC complex bound to stalled 60S ribosomal subunits. The structure establishes how Ltn1 associates with the large ribosomal subunit and properly positions its E3-catalytic RING domain to mediate nascent chain ubiquitylation. The structure also reveals that a distinguishing feature of stalled 60S particles is an exposed, nascent chain-conjugated tRNA, and that the Tae2 subunit of RQC, which facilitates Ltn1 binding, is responsible for selective recognition of stalled 60S subunits. RQC components are engaged in interactions across a large span of the 60S subunit surface, connecting the tRNA in the peptidyl transferase center to the distally located nascent chain tunnel exit. This work provides insights into a mechanism linking translation and protein degradation that targets defective proteins immediately after synthesis, while ignoring nascent chains in normally translating ribosomes. PMID:25349383

  1. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    PubMed

    Fouda, Adam; Ryde, Ulf

    2016-11-08

    We have examined how the self-interaction error in density-functional theory (DFT) calculations affects energies calculated on large systems (600-1000 atoms) involving several charged groups. We employ 18 different quantum mechanical (QM) methods, including Hartree-Fock, as well as pure, hybrid, and range-separated DFT methods. They are used to calculate reaction and activation energies for three different protein models in vacuum, in a point-charge surrounding, or with a continuum-solvent model. We show that pure DFT functionals give rise to a significant delocalization of the charges in charged groups in the protein, typically by ∼0.1 e, as evidenced from the Mulliken charges. This has a clear effect on how the surroundings affect calculated reaction and activation energies, indicating that these methods should be avoided for DFT calculations on large systems. Fortunately, methods such as CAM-B3LYP, BHLYP, and M06-2X give results that agree within a few kilojoules per mole, especially when the calculations are performed in a point-charge surrounding. Therefore, we recommend these methods to estimate the effect of the surroundings with large QM systems (but other QM methods may be used to study the intrinsic reaction and activation energies).

  2. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex.

    PubMed

    Lyumkis, Dmitry; Oliveira dos Passos, Dario; Tahara, Erich B; Webb, Kristofor; Bennett, Eric J; Vinterbo, Staal; Potter, Clinton S; Carragher, Bridget; Joazeiro, Claudio A P

    2014-11-11

    All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), composed of the listerin/Ltn1 E3 ubiquitin ligase and cofactors, mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. How RQC recognizes stalled ribosomes and performs its functions has not been understood. Using single-particle cryoelectron microscopy, we have determined the structure of the RQC complex bound to stalled 60S ribosomal subunits. The structure establishes how Ltn1 associates with the large ribosomal subunit and properly positions its E3-catalytic RING domain to mediate nascent chain ubiquitylation. The structure also reveals that a distinguishing feature of stalled 60S particles is an exposed, nascent chain-conjugated tRNA, and that the Tae2 subunit of RQC, which facilitates Ltn1 binding, is responsible for selective recognition of stalled 60S subunits. RQC components are engaged in interactions across a large span of the 60S subunit surface, connecting the tRNA in the peptidyl transferase center to the distally located nascent chain tunnel exit. This work provides insights into a mechanism linking translation and protein degradation that targets defective proteins immediately after synthesis, while ignoring nascent chains in normally translating ribosomes.

  3. Comparative visualization of protein conformations using large high resolution displays with gestures and body tracking

    NASA Astrophysics Data System (ADS)

    Marangoni, Matt; Wischgoll, Thomas

    2015-01-01

    Automatically identifying protein conformations can yield multiple candidate structures. Potential candidates are examined further to cull false positives. Individual conformations and the collection are compared when seeking flaws. Desktop displays are ineffective due to limited size and resolution. Thus a user must sacrifice large scale content by viewing the micro level with high detail or view the macro level while forfeiting small details. We address this ultimatum by utilizing multiple, high resolution displays. Using 27, 50", high resolution displays with active, stereoscopic 3D, and modified virtual environment software, each display presents a protein users can manipulate. Such an environment enables users to gain extensive insight both at the micro and macro levels when performing structural comparisons among the candidate structures. Integrating stereoscopic 3D improves the user's ability to judge conformations spatial relationships. In order to facilitate intuitive interaction, gesture recognition as well as body tracking are used. The user is able to look at the protein of interest, select a modality via gesture, and the user's motions provide intuitive navigation functions such as panning, rotating, and zooming. Using this approach, users are able to perform protein structure comparison through intuitive controls without sacrificing important visual details at any scale.

  4. Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways?

    PubMed Central

    Albenne, Cécile; Canut, Hervé; Hoffmann, Laurent; Jamet, Elisabeth

    2014-01-01

    Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes. Comparisons between these proteomes have been done based on various working strategies or different physiological stages. In this review, two points are highlighted. The first point is related to data analysis with an overview of the cell wall proteomes already described. A large body of data is now available with the description of cell wall proteomes of seventeen plant species. CWP contents exhibit particularities in relation to the major differences in cell wall composition and structure between these plants and between plant organs. The second point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components. PMID:28250379

  5. Strategy for large scale solubilization of coal-characterization of neurospora protein and gene

    SciTech Connect

    Patel, A.; Chen, Y.P.; Mishra, N.C.

    1995-12-31

    Coal represents an important source of energy. Its utilization for generating energy has been offset by environmental problem that it creates by the release of SOx and NOx, which are major causes of acid rain and deforestation. Some of these problems can be tackled by the use of industrial scrubbers. However, a biotechnological approach to these problems may prove more efficient and environment friendly. We have employed certain genetically characterized fungi for the biosolubilization of coal in order to yield chemicals that can be converted into utilizable energy and can be rendered free of SOx and NOx at the source. Here we describe the purification of a protein which is responsible for the biodegradation of low rank coal both in vivo and in vitro. We also report the characterization of the biochemical nature of the coal derived products obtained after the biosolubilization of coal by this protein in vivo and in, vitro. Identification and characterization of this fungal protein is expected to help the cloning of the gene encoding this protein which is needed to construct a super strain of Neurospora capable of large scale solubilization of coal.

  6. Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways?

    PubMed

    Albenne, Cécile; Canut, Hervé; Hoffmann, Laurent; Jamet, Elisabeth

    2014-04-17

    Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes. Comparisons between these proteomes have been done based on various working strategies or different physiological stages. In this review, two points are highlighted. The first point is related to data analysis with an overview of the cell wall proteomes already described. A large body of data is now available with the description of cell wall proteomes of seventeen plant species. CWP contents exhibit particularities in relation to the major differences in cell wall composition and structure between these plants and between plant organs. The second point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components.

  7. Transport of solutes through cartilage: permeability to large molecules.

    PubMed Central

    Maroudas, A

    1976-01-01

    A review of the transport of solutes through articular cartilage is given, with special reference to the effect of variations in matrix composition. Some physiological implications of our findings are discussed. Also, results of an experimental study of the permeability of articular cartilage to large globular proteins are presented. Because of the very low partition coefficients of large solutes between cartilage and an external solution new experimental techniques had to be devised, particularly for the study of diffusion. The partition coefficients of solutes were found to decrease very steeply with increase in size, up to serum albumin. There was, however, no further decrease for IGG. The diffusion coefficient of serum albumin in cartilage was relatively high (one quarter of the value in aqueous solution). These two facts taken together suggest that there may be a very small fraction of relatively large pores in cartilage through which the transport of large molecules is taking place. The permeability of cartilage to large molecules is extremely sensitive to variations in the glycosaminoglycan content: for a threefold increase in the latter there is a hundredfold decrease in the partition coefficient. For cartilage of fixed charge density around 0-19 m-equiv/g, there is no penetration at all of globular proteins of size equal to or larger than serum albumin. PMID:1002608

  8. Biodegradable Magnetic Silica@Iron Oxide Nanovectors with Ultra-Large Mesopores for High Protein Loading, Magnetothermal Release, and Delivery.

    PubMed

    Omar, Haneen; Croissant, Jonas G; Alamoudi, Kholod; Alsaiari, Shahad; Alradwan, Ibrahim; Majrashi, Majed A; Anjum, Dalaver H; Martins, Patricia; Moosa, Basem; Almalik, Abdulaziz; Khashab, Niveen M

    2016-11-29

    The delivery of large cargos of diameter above 15nm for biomedical applications has proved challenging since it requires biocompatible, stably-loaded, and biodegradable nanomaterials. In this study, we describe the design of biodegradable silica-iron oxide hybrid nanovectors with large mesopores for large protein delivery in cancer cells. The mesopores of the nanomaterials spanned from 20 to 60nm in diameter and post-functionalization allowed the electrostatic immobilization of large proteins (e.g. mTFP-Ferritin, ~534kDa). Half of the content of the nanovectors was based with iron oxide nanophases which allowed the rapid biodegradation of the carrier in fetal bovine serum and a magnetic responsiveness. The nanovectors released large protein cargos in aqueous solution under acidic pH or magnetic stimuli. The delivery of large proteins was then autonomously achieved in cancer cells via the silica-iron oxide nanovectors, which is thus a promising for biomedical applications.

  9. A novel tau mutation, p.K317N, causes globular glial tauopathy.

    PubMed

    Tacik, Pawel; DeTure, Michael; Lin, Wen-Lang; Sanchez Contreras, Monica; Wojtas, Aleksandra; Hinkle, Kelly M; Fujioka, Shinsuke; Baker, Matthew C; Walton, Ronald L; Carlomagno, Yari; Brown, Patricia H; Strongosky, Audrey J; Kouri, Naomi; Murray, Melissa E; Petrucelli, Leonard; Josephs, Keith A; Rademakers, Rosa; Ross, Owen A; Wszolek, Zbigniew K; Dickson, Dennis W

    2015-08-01

    Globular glial tauopathies (GGTs) are 4-repeat tauopathies neuropathologically characterized by tau-positive, globular glial inclusions, including both globular oligodendroglial inclusions and globular astrocytic inclusions. No mutations have been found in 25 of the 30 GGT cases reported in the literature who have been screened for mutations in microtubule associated protein tau (MAPT). In this report, six patients with GGT (four with subtype III and two with subtype I) were screened for MAPT mutations. They included 4 men and 2 women with a mean age at death of 73 years (55-83 years) and mean age at symptomatic onset of 66 years (50-77 years). Disease duration ranged from 5 to 14 years. All were homozygous for the MAPT H1 haplotype. Three patients had a positive family history of dementia, and a novel MAPT mutation (c.951G>C, p.K317N) was identified in one of them, a patient with subtype III. Recombinant tau protein bearing the lysine-to-asparagine substitution at amino acid residue 317 was used to assess functional significance of the variant on microtubule assembly and tau filament formation. Recombinant p.K317N tau had reduced ability to promote tubulin polymerization. Recombinant 3R and 4R tau bearing the p.K317N mutation showed decreased 3R tau and increased 4R tau filament assembly. These results strongly suggest that the p.K317N variant is pathogenic. Sequencing of MAPT should be considered in patients with GGT and a family history of dementia or movement disorder. Since several individuals in our series had a positive family history but no MAPT mutation, genetic factors other than MAPT may play a role in disease pathogenesis.

  10. Physiological and technological aspects of large-scale heterologous-protein production with yeasts.

    PubMed

    Hensing, M C; Rouwenhorst, R J; Heijnen, J J; van Dijken, J P; Pronk, J T

    1995-01-01

    Commercial production of heterologous proteins by yeasts has gained considerable interest. Expression systems have been developed for Saccharomyces cerevisiae and a number of other yeasts. Generally, much attention is paid to the molecular aspects of heterologous-gene expression. The success of this approach is indicated by the high expression levels that have been obtained in shake-flask cultures. For large-scale production however, possibilities and restrictions related to host-strain physiology and fermentation technology also have to be considered. In this review, these physiological and technological aspects have been evaluated with the aid of numerical simulations. Factors that affect the choice of a carbon substrate for large-scale production involve price, purity and solubility. Since oxygen demand and heat production (which are closely linked) limit the attainable growth rate in large-scale processes, the biomass yield on oxygen is also a key parameter. Large-scale processes impose restrictions on the expression system. Many promoter systems that work well in small-scale systems cannot be implemented in industrial environments. Furthermore, large-scale fed-batch fermentations involve a substantial number of generations. Therefore, even low expression-cassette instability has a profound effect on the overall productivity of the system. Multicopy-integration systems may provide highly stable expression systems for industrial processes. Large-scale fed-batch processes are typically performed at a low growth rate. Therefore, effects of a low growth rate on the physiology and product formation rates of yeasts are of key importance. Due to the low growth rates in the industrial process, a substantial part of the substrate carbon is expended to meet maintenance-energy requirements. Factors that reduce maintenance-energy requirements will therefore have a positive effect on product yield. The relationship between specific growth rate and specific product formation

  11. Globular adiponectin improves high glucose-suppressed endothelial progenitor cell function through endothelial nitric oxide synthase dependent mechanisms.

    PubMed

    Huang, Po-Hsun; Chen, Jia-Shiong; Tsai, Hsiao-Ya; Chen, Yung-Hsiang; Lin, Feng-Yen; Leu, Hsin-Bang; Wu, Tao-Cheng; Lin, Shing-Jong; Chen, Jaw-Wen

    2011-07-01

    Plasma levels of adiponectin, an adipose-specific protein with putative anti-atherogenic properties, could be down-regulated in obese and diabetic subjects. Recent insights suggest that the injured endothelial monolayer is regenerated by circulating endothelial progenitor cells (EPCs), but high glucose reduces number and functions of EPCs. Here, we tested the hypothesis that globular adiponectin can improve high glucose-suppressed EPC functions by restoration of endothelial nitric oxide synthase (eNOS) activity. Late EPCs isolated from healthy subjects appeared with cobblestone shape at 2-4 weeks. EPCs were incubated with high glucose (25 mM) and treatment with globular adiponectin for functional study. Migration and tube formation assays were used to evaluate the vasculogenetic capacity of EPCs. The activities of eNOS, Akt and concentrations of nitric oxide (NO) were also determined. Administration of globular adiponectin at physiological concentrations promoted EPC migration and tube formation, and dose-dependently upregulated phosphorylation of eNOS, Akt and augmented NO production. Chronic incubation of EPCs in high-glucose medium significantly impaired EPC function and induced cellular senescence, but these suppression effects were reversed by treatment with globular adiponectin. Globular adiponectin reversed high glucose-impaired EPC functions through NO- and p38 MAPK-related mechanisms. In addition, nude mice that received EPCs treated with adiponectin in high glucose medium showed a significant improvement in blood flow than those received normal saline and EPCs incubated in high glucose conditions. The administration of globular adiponectin improved high glucose-impaired EPC functions in vasculogenesis by restoration of eNOS activity. These beneficial effects may provide some novel rational to the vascular protective properties of adiponectin.

  12. Edades relativas de cúmulos globulares

    NASA Astrophysics Data System (ADS)

    Miller Bertolami, M.; Forte, J. C.

    El trabajo de Rossemberg et al (1999), estudia las edades relativas de cúmulos globulares galácticos mediante el análisis de ciertos parámetros morfológicos de los diagramas color-magnitud de dichos cúmulos. Este trabajo se centra en tres puntos: analizar la consistencia de los resultados obtenidos por Rossemberg et al (1999) al emplear observaciones en el sistema fotométrico de Washington, más precisamente, las magnitudes C y T1 en lugar de las magnitudes V e I utilizadas por dichos autores. De la existencia de colores integrados, metalicidad y edad (relativa) para 21 de los cúmulos utilizados en dicho trabajo, se analiza la consistencia de estos resultados con las dependencias de color integrado como función de la edad y la metalicidad que se desprenden de los modelos teóricos de luz integrada por Worthey (1994), Schulz (2002) y Lee et al (2002). Por último se lleva a cabo una breve comparación de la morfología de los diagramas color-magnitud de los cúmulos globulares y de las isocronas utilizadas, a fin de intentar identificar algunas de las posibles causas de las diferencias observadas en los incisos anteriores.

  13. A large iris-like expansion of a mechanosensitive channel protein induced by membrane tension

    NASA Technical Reports Server (NTRS)

    Betanzos, Monica; Chiang, Chien-Sung; Guy, H. Robert; Sukharev, Sergei

    2002-01-01

    MscL, a bacterial mechanosensitive channel of large conductance, is the first structurally characterized mechanosensor protein. Molecular models of its gating mechanisms are tested here. Disulfide crosslinking shows that M1 transmembrane alpha-helices in MscL of resting Escherichia coli are arranged similarly to those in the crystal structure of MscL from Mycobacterium tuberculosis. An expanded conformation was trapped in osmotically shocked cells by the specific bridging between Cys 20 and Cys 36 of adjacent M1 helices. These bridges stabilized the open channel. Disulfide bonds engineered between the M1 and M2 helices of adjacent subunits (Cys 32-Cys 81) do not prevent channel gating. These findings support gating models in which interactions between M1 and M2 of adjacent subunits remain unaltered while their tilts simultaneously increase. The MscL barrel, therefore, undergoes a large concerted iris-like expansion and flattening when perturbed by membrane tension.

  14. Exploiting large-scale drug-protein interaction information for computational drug repurposing

    PubMed Central

    2014-01-01

    Background Despite increased investment in pharmaceutical research and development, fewer and fewer new drugs are entering the marketplace. This has prompted studies in repurposing existing drugs for use against diseases with unmet medical needs. A popular approach is to develop a classification model based on drugs with and without a desired therapeutic effect. For this approach to be statistically sound, it requires a large number of drugs in both classes. However, given few or no approved drugs for the diseases of highest medical urgency and interest, different strategies need to be investigated. Results We developed a computational method termed “drug-protein interaction-based repurposing” (DPIR) that is potentially applicable to diseases with very few approved drugs. The method, based on genome-wide drug-protein interaction information and Bayesian statistics, first identifies drug-protein interactions associated with a desired therapeutic effect. Then, it uses key drug-protein interactions to score other drugs for their potential to have the same therapeutic effect. Conclusions Detailed cross-validation studies using United States Food and Drug Administration-approved drugs for hypertension, human immunodeficiency virus, and malaria indicated that DPIR provides robust predictions. It achieves high levels of enrichment of drugs approved for a disease even with models developed based on a single drug known to treat the disease. Analysis of our model predictions also indicated that the method is potentially useful for understanding molecular mechanisms of drug action and for identifying protein targets that may potentiate the desired therapeutic effects of other drugs (combination therapies). PMID:24950817

  15. In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces.

    PubMed

    Wu, Zhonghua; Hu, Gang; Yang, Jianyi; Peng, Zhenling; Uversky, Vladimir N; Kurgan, Lukasz

    2015-09-14

    We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins. These result are applicable for proteins involved in interaction with DNA, RNA, and proteins and suggest that disordered proteins and binding regions are less compact and more likely to assume extended shape. We demonstrate that disordered protein binding residues in the interfaces of disordered proteins drive the increase in the per residue area of these interfaces. Our results can be used to predict in silico whether a given protomer from the DNA, RNA or protein complex is likely to be disordered in its unbound form.

  16. Neutrino and axion bounds from the globular cluster M5 (NGC 5904).

    PubMed

    Viaux, N; Catelan, M; Stetson, P B; Raffelt, G G; Redondo, J; Valcarce, A A R; Weiss, A

    2013-12-06

    The red-giant branch (RGB) in globular clusters is extended to larger brightness if the degenerate helium core loses too much energy in "dark channels." Based on a large set of archival observations, we provide high-precision photometry for the Galactic globular cluster M5 (NGC 5904), allowing for a detailed comparison between the observed tip of the RGB with predictions based on contemporary stellar evolution theory. In particular, we derive 95% confidence limits of g(ae)<4.3×10(-13) on the axion-electron coupling and μ(ν)<4.5×10(-12)μ(B) (Bohr magneton μ(B)=e/2m(e)) on a neutrino dipole moment, based on a detailed analysis of statistical and systematic uncertainties. The cluster distance is the single largest source of uncertainty and can be improved in the future.

  17. mBeRFP, an improved large stokes shift red fluorescent protein.

    PubMed

    Yang, Jie; Wang, Liang; Yang, Fei; Luo, Haiming; Xu, Lingling; Lu, Jinling; Zeng, Shaoqun; Zhang, Zhihong

    2013-01-01

    Herein, we describe the generation of a monomeric large Stokes shift (LSS) red fluorescent protein, mBeRFP, with excitation and emission peaks at 446 and 615 nm, respectively. Compared with two previously reported LSS-RFPs (mKeima and LSS-mKate2), mBeRFP is approximately three times brighter. In addition, mBeRFP is characterized by improved photostability, rapid maturation, an extended lifetime, and a monomeric nature. Additionally, mBeRFP can be paired with the Alexa 647 dye as a FRET donor to detect caspase 3 activity. This FRET pair has an extremely dynamic range and a large Förster radius (approximately 6.5 nm). To demonstrate the applicability of mBeRFP for imaging in living cells, we performed dual-color imaging of mBeRFP and CFP simultaneously excited by a single excitation source, and we demonstrated that these fluorescent proteins allow the clear visualization of the dynamics of Bax during cancer cell apoptosis. Thus, mBeRFP appears to be particularly useful for cellular imaging applications.

  18. Protein crystal growth in microgravity: Temperature induced large scale crystallization of insulin

    NASA Technical Reports Server (NTRS)

    Long, Marianna M.; Delucas, Larry J.; Smith, C.; Carson, M.; Moore, K.; Harrington, Michael D.; Pillion, D. J.; Bishop, S. P.; Rosenblum, W. M.; Naumann, R. J.

    1994-01-01

    One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macro-molecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjuction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.

  19. QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families

    PubMed Central

    Gudyś, Adam; Deorowicz, Sebastian

    2017-01-01

    The ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins. PMID:28139687

  20. Monoaminergic modulation of GABAergic transmission onto cerebellar globular cells.

    PubMed

    Hirono, Moritoshi; Nagao, Soichi; Yanagawa, Yuchio; Konishi, Shiro

    2017-03-11

    Cerebellar Purkinje cells (PCs) project their axon collaterals to underneath of the PC layer and make GABAergic synaptic contacts with globular cells, a subgroup of Lugaro cells. GABAergic transmission derived from the PC axon collaterals is so powerful that it could inhibit globular cells and regulate their firing patterns. However, the physiological properties and implications of the GABAergic synapses on globular cells remain unknown. Using whole-cell patch-clamp recordings from globular cells in the mouse cerebellum, we examined the monoaminergic modulation of GABAergic inputs to these cells. Application of either serotonin (5-HT) or noradrenaline (NA) excited globular cells, thereby leading to their firing. The 5-HT- and NA-induced firing was temporally confined and attenuated by GABAergic transmission, although 5-HT and NA exerted an inhibitory effect on the release of GABA from presynaptic terminals of PC axon collaterals. Agonists for 5-HT1B receptors and α2-adrenoceptors mimicked the 5-HT- and NA-induced suppression of GABAergic activity. Through their differential modulatory actions on the cerebellar inhibitory neural circuits, 5-HT facilitated PC firing, whereas NA suppressed it. These results indicate that 5-HT and NA regulate the membrane excitability of globular cells and PCs through their differential modulation of not only the membrane potential but also GABAergic synaptic circuits. Monoaminergic modulation of the neural connections between globular cells and PCs could play a role in cerebellar motor coordination.

  1. Globular cluster systems in nearby dwarf galaxies - III. Formation efficiencies of old globular clusters

    NASA Astrophysics Data System (ADS)

    Georgiev, Iskren Y.; Puzia, Thomas H.; Goudfrooij, Paul; Hilker, Michael

    2010-08-01

    We investigate the origin of the shape of the globular cluster (GC) system scaling parameters as a function of galaxy mass, i.e. specific frequency (SN), specific luminosity (SL), specific mass (SM) and specific number () of GCs. In the low-mass galaxy regime (MV >~ -16 mag), our analysis is based on Hubble Space Telescope/Advanced Camera for Surveys observations of GC populations of faint, mainly late-type dwarf galaxies in low-density environments. In order to sample the entire range in galaxy mass (MV = -11 to -23mag =106- 1011Lsolar), environment and morphology we augment our sample with data of spiral and elliptical galaxies from the literature, in which old GCs are reliably detected. This large data set confirms (irrespective of the galaxy type) the increase in the specific frequencies of GCs above and below a galaxy magnitude of MV ~= -20mag. Over the full mass range, the SL value of early-type galaxies is, on average, twice that of late types. To investigate the observed trends, we derive theoretical predictions of GC system scaling parameters as a function of host galaxy mass based on the models of Dekel and Birnboim in which star formation processes are regulated by stellar and supernova feedback below a stellar mass of 3 × 1010Msolar and by virial shocks above it. We find that the analytical model describes remarkably well the shape of the GC system scaling parameter distributions with a universal specific GC formation efficiency, η, which relates the total mass in GCs to the total galaxy halo mass. Early-type and late-type galaxies show a similar mean value of η = 5.5 × 10-5, with an increasing scatter towards lower galaxy masses. This can be due to the enhanced stochastic nature of the star and star-cluster formation processes for such systems. Some massive galaxies have excess η values compared to what is expected from the mean model prediction for galaxies more luminous than MV ~= -20mag (LV >~ 1010Lsolar). This may be attributed to a very

  2. THE GLOBULAR CLUSTER SYSTEM OF NGC 4636 AND FORMATION OF GLOBULAR CLUSTERS IN GIANT ELLIPTICAL GALAXIES

    SciTech Connect

    Park, Hong Soo; Lee, Myung Gyoon; Hwang, Ho Seong; Kim, Sang Chul; Arimoto, Nobuo; Yamada, Yoshihiko; Tamura, Naoyuki; Onodera, Masato E-mail: mglee@astro.snu.ac.kr E-mail: sckim@kasi.re.kr E-mail: yoshihiko.yamada@nao.ac.jp E-mail: monodera@phys.ethz.ch

    2012-11-10

    We present a spectroscopic analysis of the metallicities, ages, and alpha-elements of the globular clusters (GCs) in the giant elliptical galaxy (gE) NGC 4636 in the Virgo Cluster. Line indices of the GCs are measured from the integrated spectra obtained with Faint Object Camera and Spectrograph on the Subaru 8.2 m Telescope. We derive [Fe/H] values of 59 GCs based on the Brodie and Huchra method, and [Z/H], age, and [{alpha}/Fe] values of 33 GCs from the comparison of the Lick line indices with single stellar population models. The metallicity distribution of NGC 4636 GCs shows a hint of a bimodality with two peaks at [Fe/H] = -1.23({sigma} = 0.32) and -0.35({sigma} = 0.19). The age spread is large from 2 Gyr to 15 Gyr and the fraction of young GCs with age <5 Gyr is about 27%. The [{alpha}/Fe] of the GCs shows a broad distribution with a mean value [{alpha}/Fe] Almost-Equal-To 0.14 dex. The dependence of these chemical properties on the galactocentric radius is weak. We also derive the metallicities, ages, and [{alpha}/Fe] values for the GCs in other nearby gEs (M87, M49, M60, NGC 5128, NGC 1399, and NGC 1407) from the line index data in the literature using the same methods as used for NGC 4636 GCs. The metallicity distribution of GCs in the combined sample of seven gEs including NGC 4636 is found to be bimodal, supported by the KMM test with a significance level of >99.9%. All these gEs harbor some young GCs with ages less than 5 Gyr. The mean age of the metal-rich GCs ([Fe/H] >-0.9) is about 3 Gyr younger than that of the metal-poor GCs. The mean value of [{alpha}/Fe] of the gE GCs is smaller than that of the Milky Way GCs. We discuss these results in the context of GC formation in gEs.

  3. Individual globular domains and domain unfolding visualized in overstretched titin molecules with atomic force microscopy.

    PubMed

    Mártonfalvi, Zsolt; Kellermayer, Miklós

    2014-01-01

    Titin is a giant elastomeric protein responsible for the generation of passive muscle force. Mechanical force unfolds titin's globular domains, but the exact structure of the overstretched titin molecule is not known. Here we analyzed, by using high-resolution atomic force microscopy, the structure of titin molecules overstretched with receding meniscus. The axial contour of the molecules was interrupted by topographical gaps with a mean width of 27.7 nm that corresponds well to the length of an unfolded globular (immunoglobulin and fibronectin) domain. The wide gap-width distribution suggests, however, that additional mechanisms such as partial domain unfolding and the unfolding of neighboring domain multimers may also be present. In the folded regions we resolved globules with an average spacing of 5.9 nm, which is consistent with a titin chain composed globular domains with extended interdomain linker regions. Topographical analysis allowed us to allocate the most distal unfolded titin region to the kinase domain, suggesting that this domain systematically unfolds when the molecule is exposed to overstretching forces. The observations support the prediction that upon the action of stretching forces the N-terminal ß-sheet of the titin kinase unfolds, thus exposing the enzyme's ATP-binding site and hence contributing to the molecule's mechanosensory function.

  4. Sulphur in the metal poor globular cluster NGC 6397

    NASA Astrophysics Data System (ADS)

    Koch, A.; Caffau, E.

    2011-10-01

    Sulphur (S) is a non-refractory α-element that is not locked into dust grains in the interstellar medium. Thus no correction to the measured, interstellar sulphur abundance is needed and it can be readily compared to the S content in stellar photospheres. Here we present the first measurement of sulphur in the metal poor globular cluster (GC) NGC 6397, as detected in a MIKE/Magellan high signal-to-noise, high-resolution spectrum of one red giant star. While abundance ratios of sulphur are available for a larger number of Galactic stars down to an [Fe/H] of ~ -3.5 dex, no measurements in globular clusters more metal poor than -1.5 dex have been reported so far. We find aNLTE, 3-D abundance ratio of [S/Fe] = +0.52 ± 0.20 (stat.) ± 0.08 (sys.), based on theS I, Multiplet 1 line at 9212.8 Å. This value is consistent with a Galactic halo plateau as typical of other α-elements in GCs and field stars, but we cannot rule out its membership with a second branch of increasing [S/Fe] with decreasing [Fe/H], claimed in the literature, which leads to a large scatter at metallicities around - 2 dex. The [S/Mg] and [S/Ca] ratios in this star are compatible with a Solar value to within the (large) uncertainties. Despite the very large scatter in these ratios across Galactic stars between literature samples, this indicates that sulphur traces the chemical imprints of the other α-elements in metal poor GCs. Combined with its moderate sodium abundance ([S/Na]NLTE = 0.48), the [S/Fe] ratio in this GC extends a global, positive S-Na correlation that is not seen in field stars and might indicate that proton-capture reactions contributed to the production of sulphur in the (metal poor) early GC environments. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  5. Efectos de mareas en cúmulos globulares

    NASA Astrophysics Data System (ADS)

    Ramos, F.; Coenda, V.; Muriel, H.; Abadi, M.

    Using an N-body numerical simulation in the framework of the CDM cosmological model we study the globular cluster population in a simulated galaxy cluster. We select particles that trace the bimodal (red and blue) globular cluster system of each individual dark matter halo prior to their incorporation to the cluster virial radius. We found that the blue population is more prone to be removed from the halo than the red one. This result suggests that globular clusters are tidally disrupted; being the blue (more extended) population easily removed. FULL TEXT IN SPANISH

  6. Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR

    PubMed Central

    Lee, Sang-Won; Berger, Scott J.; Martinović, Suzana; Paša-Tolić, Ljiljana; Anderson, Gordon A.; Shen, Yufeng; Zhao, Rui; Smith, Richard D.

    2002-01-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry coupled with capillary reverse-phase liquid chromatography was used to characterize intact proteins from the large subunit of the yeast ribosome. High mass measurement accuracy, achieved by “mass locking” with an internal standard from a dual electrospray ionization source, allowed identification of ribosomal proteins. Analyses of the intact proteins revealed information on cotranslational and posttranslational modifications of the ribosomal proteins that included loss of the initiating methionine, acetylation, methylation, and proteolytic maturation. High-resolution separations permitted differentiation of protein isoforms having high structural similarity as well as proteins from their modified forms, facilitating unequivocal assignments. The study identified 42 of the 43 core large ribosomal subunit proteins and 58 (of 64 possible) core large subunit protein isoforms having unique masses in a single analysis. These results demonstrate the basis for the high-throughput analyses of complex mixtures of intact proteins, which we believe will be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations. PMID:11983894

  7. BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures

    NASA Astrophysics Data System (ADS)

    Sarti, E.; Zamuner, S.; Cossio, P.; Laio, A.; Seno, F.; Trovato, A.

    2013-12-01

    In protein structure prediction it is of crucial importance, especially at the refinement stage, to score efficiently large sets of models by selecting the ones that are closest to the native state. We here present a new computational tool, BACHSCORE, that allows its users to rank different structural models of the same protein according to their quality, evaluated by using the BACH++ (Bayesian Analysis Conformation Hunt) scoring function. The original BACH statistical potential was already shown to discriminate with very good reliability the protein native state in large sets of misfolded models of the same protein. BACH++ features a novel upgrade in the solvation potential of the scoring function, now computed by adapting the LCPO (Linear Combination of Pairwise Orbitals) algorithm. This change further enhances the already good performance of the scoring function. BACHSCORE can be accessed directly through the web server: bachserver.pd.infn.it. Catalogue identifier: AEQD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQD_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 130159 No. of bytes in distributed program, including test data, etc.: 24 687 455 Distribution format: tar.gz Programming language: C++. Computer: Any computer capable of running an executable produced by a g++ compiler (4.6.3 version). Operating system: Linux, Unix OS-es. RAM: 1 073 741 824 bytes Classification: 3. Nature of problem: Evaluate the quality of a protein structural model, taking into account the possible “a priori” knowledge of a reference primary sequence that may be different from the amino-acid sequence of the model; the native protein structure should be recognized as the best model. Solution method: The contact potential scores the occurrence of any given type of residue pair in 5 possible

  8. Rosat Observations of Nine Globular Clusters

    NASA Technical Reports Server (NTRS)

    Rappaport, S.; Dewey, D.; Levine, A.; Macri, L.

    1994-01-01

    The ROSAT HRI was used to image fields around nine Galactic globular clusters that have central densities in the range of 10(exp 4) - 10(exp 5) solar mass pc(exp -3) and that had not previously been observed with the Einstein Observatory. We detected X-ray sources associated with Pal 2 and NGC 6304 with luminosities of 1.1 x 10(exp 34) ergs/s and 1.2 x 10(exp 33) ergs/s, respectively. No X-ray emission was detected from the source in Ter 6, thus confirming its transient nature. In all, there were 23 serendipitous sources found in the nine fields; none was apparently associated with any of the other seven clusters. The results are discussed in the context of low-luminosity cluster X-ray sources, in general.

  9. BLUE STRAGGLERS IN GLOBULAR CLUSTER 47 TUCANAE

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The core of globular cluster 47 Tucanae is home to many blue stragglers, rejuvenated stars that glow with the blue light of young stars. A ground-based telescope image (on the left) shows the entire crowded core of 47 Tucanae, located 15,000 light-years away in the constellation Tucana. Peering into the heart of the globular cluster's bright core, the Hubble Space Telescope's Wide Field and Planetary Camera 2 separated the dense clump of stars into many individual stars (image on right). Some of these stars shine with the light of old stars; others with the blue light of blue stragglers. The yellow circles in the Hubble telescope image highlight several of the cluster's blue stragglers. Analysis for this observation centered on one massive blue straggler. Astronomers theorize that blue stragglers are formed either by the slow merger of stars in a double-star system or by the collision of two unrelated stars. For the blue straggler in 47 Tucanae, astronomers favor the slow merger scenario. This image is a 3-color composite of archival Hubble Wide Field and Planetary Camera 2 images in the ultraviolet (blue), blue (green), and violet (red) filters. Color tables were assigned and scaled so that the red giant stars appear orange, main-sequence stars are white/green, and blue stragglers are appropriately blue. The ultraviolet images were taken on Oct. 25, 1995, and the blue and violet images were taken on Sept. 1, 1995. Credit: Rex Saffer (Villanova University) and Dave Zurek (STScI), and NASA

  10. LITHIUM-RICH GIANTS IN GLOBULAR CLUSTERS

    SciTech Connect

    Kirby, Evan N.; Cohen, Judith G.; Guhathakurta, Puragra; Hong, Jerry; Guo, Michelle; Guo, Rachel; Cunha, Katia

    2016-03-10

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron–Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval.

  11. Lithium-rich Giants in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Kirby, Evan N.; Guhathakurta, Puragra; Zhang, Andrew J.; Hong, Jerry; Guo, Michelle; Guo, Rachel; Cohen, Judith G.; Cunha, Katia

    2016-03-01

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron-Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval. The data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

  12. Analysis of the large (L) protein gene of the porcine rubulavirus LPMV: identification of possible functional domains.

    PubMed

    Svenda, M; Berg, M; Moreno-López, J; Linné, T

    1997-04-01

    The complete nucleotide sequence of the porcine rubulavirus LPMV (La Piedad Michoacan virus) large (L) protein gene was determined and analysed. The L mRNA was found to span 6,786 nucleotides, containing one single large open reading frame (ORF), putatively encoding a polypeptide of 2,251 amino acids. By aligning the amino acid sequence of the LPMV L-protein with L-protein of a number of viruses belonging to the order mononegavirale, a high degree of similarity between the LPMV L-protein and other rubula virus L-proteins was demonstrated, extending through almost the whole protein. Additionally we could identify several regions as being highly conserved among all studied viruses of the order mononegavirale. The significance of these regions are discussed.

  13. A DYING STAR IN GLOBULAR CLUSTER

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A DYING STAR IN GLOBULAR CLUSTER M15 The globular cluster Messier 15 is shown in this color image obtained with the NASA Hubble Space Telescope's Wide Field Planetary Camera 2 (WFPC2). Lying some 40,000 light-years from Earth in the direction of the constellation Pegasus, M15 is one of nearly 150 known globular clusters that form a vast halo surrounding our Milky Way galaxy. Each of these clusters is a spherical association of hundreds of thousands of ancient stars. The image, prepared by the Hubble Heritage team, attempts to show the stars in M15 in their true colors. The brightest cluster stars are red giants, with an orange color due to surface temperatures lower than our Sun's. Most of the fainter stars are hotter, giving them a bluish-white color. If we lived in the core of M15, our sky would blaze with tens of thousands of brilliant stars both day and night! Nestled among the myriads of stars visible in the Hubble image is an astronomical oddity. The pinkish object to the upper left of the cluster's core is a gas cloud surrounding a dying star. Known as Kuestner 648, this was the first planetary nebula to be identified in a globular cluster. In 1928, F. G. Pease, working at the 100-inch telescope of California's Mount Wilson Observatory, photographed the spectrum of K 648 and discovered the telltale bright emission of a nebular gas cloud rather than a normal star. In the ensuing 70 years, only three more planetary nebulae have been discovered in globular clusters. The stars in M15 and other globular clusters are estimated to be about 12 billion years old. They were among the first generations of stars to form in the Milky Way. Our Sun, by comparison, is a youthful 4.6 billion years old. As a star like the Sun ages, it exhausts the hydrogen that fuels its nuclear fusion, and increases in size to become a red giant. Then it ejects its outer layers into space, producing a planetary nebula. The remnant star at the center of the nebula gradually dies away as a

  14. A DYING STAR IN GLOBULAR CLUSTER

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A DYING STAR IN GLOBULAR CLUSTER M15 The globular cluster Messier 15 is shown in this color image obtained with the NASA Hubble Space Telescope's Wide Field Planetary Camera 2 (WFPC2). Lying some 40,000 light-years from Earth in the direction of the constellation Pegasus, M15 is one of nearly 150 known globular clusters that form a vast halo surrounding our Milky Way galaxy. Each of these clusters is a spherical association of hundreds of thousands of ancient stars. The image, prepared by the Hubble Heritage team, attempts to show the stars in M15 in their true colors. The brightest cluster stars are red giants, with an orange color due to surface temperatures lower than our Sun's. Most of the fainter stars are hotter, giving them a bluish-white color. If we lived in the core of M15, our sky would blaze with tens of thousands of brilliant stars both day and night! Nestled among the myriads of stars visible in the Hubble image is an astronomical oddity. The pinkish object to the upper left of the cluster's core is a gas cloud surrounding a dying star. Known as Kuestner 648, this was the first planetary nebula to be identified in a globular cluster. In 1928, F. G. Pease, working at the 100-inch telescope of California's Mount Wilson Observatory, photographed the spectrum of K 648 and discovered the telltale bright emission of a nebular gas cloud rather than a normal star. In the ensuing 70 years, only three more planetary nebulae have been discovered in globular clusters. The stars in M15 and other globular clusters are estimated to be about 12 billion years old. They were among the first generations of stars to form in the Milky Way. Our Sun, by comparison, is a youthful 4.6 billion years old. As a star like the Sun ages, it exhausts the hydrogen that fuels its nuclear fusion, and increases in size to become a red giant. Then it ejects its outer layers into space, producing a planetary nebula. The remnant star at the center of the nebula gradually dies away as a

  15. Globular clusters in the inner regions of NGC 5128 (CENTAURUS A)

    SciTech Connect

    Minniti, D. |; Alonso, M.V.; Goudfrooij, P.; Jablonka, P.; Meylan, G.

    1996-08-01

    We have identified 26 new globular cluster candidates in the inner 3 kpc of NGC 5128 (Centaurus A), the nearest known large galaxy that is the probable product of a merger. The clusters are selected on the basis of their structural parameters (observed core diameters and ellipticities), as measured from archival Wide Field Planetary Camera (WFPC) {ital Hubble} {ital Space} {ital Telescope} ({ital HST}) images. IR photometry obtained with IRAC2B at the ESO/MPI 2.2 m telescope is combined with the optical HST photometry. Most of these clusters have normal colors typical of old globular clusters like those found in the Milky Way and M31. We estimate their metal abundances based on the {ital R}{minus}{ital K}{sub 0} color, confirming the existence of a metallicity gradient in the inner regions of NGC 5128. The presence of metal-rich globular clusters suggests that one of the colliding galaxies was a bulge-dominated galaxy ({ital E} or early {ital S}). A few clusters have colors and magnitudes similar to intermediate-age clusters containing carbon stars in the Magellanic Clouds. If the intermediate-age clusters were formed during a merger, then this episode must have occurred a few gigayears ago. Alternatively, we are looking at the cluster members of one of the colliding galaxies, which would then have been a late-type disk galaxy. {copyright} {ital 1996 The American Astronomical Society.}

  16. Measuring consistent masses for 25 Milky Way globular clusters

    SciTech Connect

    Kimmig, Brian; Seth, Anil; Ivans, Inese I.; Anderton, Tim; Gregersen, Dylan; Strader, Jay; Caldwell, Nelson

    2015-02-01

    We present central velocity dispersions, masses, mass-to-light ratios (M/Ls ), and rotation strengths for 25 Galactic globular clusters (GCs). We derive radial velocities of 1951 stars in 12 GCs from single order spectra taken with Hectochelle on the MMT telescope. To this sample we add an analysis of available archival data of individual stars. For the full set of data we fit King models to derive consistent dynamical parameters for the clusters. We find good agreement between single-mass King models and the observed radial dispersion profiles. The large, uniform sample of dynamical masses we derive enables us to examine trends of M/L with cluster mass and metallicity. The overall values of M/L and the trends with mass and metallicity are consistent with existing measurements from a large sample of M31 clusters. This includes a clear trend of increasing M/L with cluster mass and lower than expected M/Ls for the metal-rich clusters. We find no clear trend of increasing rotation with increasing cluster metallicity suggested in previous work.

  17. Semi-rigidity vs. flexibility in collective variables preselection for metadynamics studies of large proteins

    NASA Astrophysics Data System (ADS)

    Ilieva, N.; Lilkova, E.; Petkov, P.; Litov, L.

    2016-10-01

    In silico investigations of biological molecules rely on the adequate sampling of the systems' conformation space. In the case of large systems, this is a highly non trivial task, which requires the development and refinement of enhanced sampling techniques. Metadynamics — one of these techniques — is based on computation of the free energy of the system as a function of a small set of collective variables (CVs) that are assumed to be able to adequately describe the investigated process. No standard procedures or selection criteria exist for the selection of the optimal set of collective variables. The purpose of our work is to develop a CV selection protocol based on the conformational rigidity of the protein in the most sensitive for the investigated process domains. The structure identification is performed using the spatiotemporal multistage consensus clustering (SMCC), with an appropriate selection of the algorithm parameters.

  18. Parâmetros astrofísicos de estrelas gigantes do aglomerado globular 47 Tucanae

    NASA Astrophysics Data System (ADS)

    Alves-Brito, A.; Barbuy, B.

    2003-08-01

    Os aglomerados globulares são considerados laboratórios astrofísicos para a verificação da teoria de evolução estelar, bem como a trajetória químio-dinâmica das galáxias hospedeiras. Em particular, 47 Tucanae (NGC 104) configura-se como um dos mais extensivamente estudados aglomerados globulares da Galáxia devido a relativa proximidade ao Sol (R¤ = 4.5 kpc) e alta latitute galáctica (b = -44°,89). Neste trabalho, apresentamos a velocidade radial heliocêntrica e os parâmetros atmosféricos (Teff, logg, [Fe/H]) de 5 estrelas gigantes do aglomerado globular 47 Tucanae. Os espectros foram obtidos pelo espectrógrafo UVES (Ultaviolet Visual Echelle Spectrograph) de alta resolução (R = 60000) e alta razão sinal-ruído (S/N > 200), acoplado ao telescópio de 8,2m Kueyen do VLT (Very Large Telescope). Nós encontramos = -22,43 +/- 3,97 km/s, [Fe/H] ~ -0.7, 1,2 < logg < 2,2 e 4100 < Teff < 4570 para a nossa amostra. As estrelas cobrem um intervalo de magnitude 12,2 < V < 14,2. Os parâmetros atmosféricos são fundamentais para a construção de espectros sintéticos de outros aglomerados globulares ricos em metais. Trabalho financiado pela FAPESP e pelo CNPq.

  19. Functional response of healthy and diseased glomeruli to a large, protein-rich meal.

    PubMed Central

    Chan, A Y; Cheng, M L; Keil, L C; Myers, B D

    1988-01-01

    Differential solute clearances and hormone assays were used to characterize the effect of a large, protein-rich meal (1.5 g/kg) on glomerular function in 12 healthy volunteers (group I) and 12 patients with chronic glomerular disease (group II). Changes from baseline during 3 h after the meal included an elevation of plasma osmolality, progressive urinary concentration, and increasingly positive fluid balance. Plasma renin activity and arginine vasopressin levels (measured in group II only) increased significantly. Nevertheless, the rate of peak postmeal renal plasma flow became elevated by 13 and 33% in groups I and II, respectively. Corresponding peak increases in postmeal glomerular filtration rate exceeded baseline by 10 and 16%. In the proteinuric subjects of group II the fractional clearances of albumin, IgG and uncharged dextrans in the radius interval 36-54 A, declined significantly after the meal. A similar depression of the fractional dextran-clearance profile was observed also in group I. Applying the fractional clearances of relatively permeant dextrans (radii less than or equal to 44 A) to a model of hindered solute transport through an isoporous membrane, we estimate that transmembrane hydraulic pressure difference increased by 12% in group I and by between 0 to 12% in group II after protein ingestion. We conclude (i) that oral protein ingestion increases glomerular ultrafiltration pressure and rate in both normal and diseased glomeruli, (ii) that this hemodynamic response may be mediated in part by the glomerulopressor hormones angiotensin II and arginine vasopressin, and (iii) that the foregoing hemodynamic changes exert no acute adverse effect on glomerular barrier size-selectivity. PMID:3275694

  20. Ribosomal protein L3 functions as a ‘rocker switch’ to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea

    PubMed Central

    Meskauskas, Arturas

    2008-01-01

    Although ribosomal RNAs (rRNAs) comprise the bulk of the ribosome and carry out its main functions, ribosomal proteins also appear to play important structural and functional roles. Many ribosomal proteins contain long, nonglobular domains that extend deep into the rRNA cores. In eukaryotes and Archaea, ribosomal protein L3 contains two such extended domains tethered to a common globular hub, thus providing an excellent model to address basic questions relating to ribosomal protein structure/function relationships. Previous work in our laboratory identified the central ‘W-finger’ extension of yeast L3 in helping to coordinate ribosomal functions. New studies on the ‘N-terminal’ extension in yeast suggest that it works with the W-finger to coordinate opening and closing of the corridor through which the 3′ end of aa-tRNA moves during the process of accommodation. Additionally, the effect of one of the L3 N-terminal extension mutants on the interaction between C75 of the aa-tRNA and G2921 (Escherichia coli G2553) of 25S rRNA provides the first evidence of the effect of a ribosomal protein on aa-tRNA positioning and peptidyltransfer, possibly through the induced fit model. A model is presented describing how all three domains of L3 may function together as a ‘rocker switch’ to coordinate the stepwise processes of translation elongation. PMID:18832371

  1. Survey of large protein complexes D. vulgaris reveals great structural diversity

    SciTech Connect

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  2. Large Variation in Detection of Histidine-Rich Protein 2 in Plasmodium falciparum Isolates from Colombia

    PubMed Central

    Pava, Zuleima; Echeverry, Diego F.; Díaz, Gustavo; Murillo, Claribel

    2010-01-01

    Most rapid diagnostic tests (RDTs) available use histidine-rich protein 2 (HRP2) as a target. However, it has been reported that sequence variations of this protein affects its sensitivity. Currently, there is insufficient evidence for HRP2 variability in Plasmodium falciparum isolates from Colombia and its relationship with RDT performance. To determine possible geographic differences and their effects on the performance of RDTs, 22 blood samples from patients with P. falciparum malaria from Tumaco and Buenaventura, Colombia were assessed by measurement of HRP2 concentration by an HRP2 enzyme-linked immunosorbent assay, RDTs, and thick blood smear. Statistical analysis showed an association between RDT performance and HRP2 concentrations. No significant difference was found between locations. A large variation of antigen concentration in samples was found at same parasitemia. In contrast to previously reports, there was no correlation between initial parasitemia and HRP2 concentration. Our results indicate that antigen quantity should be studied more carefully because the sensitivity of the RDT is affected more by antigen concentration than by parasitemia. PMID:20889875

  3. Target-Based Drug Repositioning Using Large-Scale Chemical-Protein Interactome Data.

    PubMed

    Sawada, Ryusuke; Iwata, Hiroaki; Mizutani, Sayaka; Yamanishi, Yoshihiro

    2015-12-28

    Drug repositioning, or the identification of new indications for known drugs, is a useful strategy for drug discovery. In this study, we developed novel computational methods to predict potential drug targets and new drug indications for systematic drug repositioning using large-scale chemical-protein interactome data. We explored the target space of drugs (including primary targets and off-targets) based on chemical structure similarity and phenotypic effect similarity by making optimal use of millions of compound-protein interactions. On the basis of the target profiles of drugs, we constructed statistical models to predict new drug indications for a wide range of diseases with various molecular features. The proposed method outperformed previous methods in terms of interpretability, applicability, and accuracy. Finally, we conducted a comprehensive prediction of the drug-target-disease association network for 8270 drugs and 1401 diseases and showed biologically meaningful examples of newly predicted drug targets and drug indications. The predictive model is useful to understand the mechanisms of the predicted drug indications.

  4. Characterizing detergent mediated reconstitution of viral protein M2 in large unilamellar vesicles

    NASA Astrophysics Data System (ADS)

    Freyre, Mariel; Grossman, Carl; Crouch, Catherine; Howard, Kathleen

    2015-03-01

    Influenza M2 is a model membrane protein whose function is to induce curvature and vesicle formation in the process of viral infection. To study embedded M2 in synthetic phospholipid vesicles (large unilamellar vesicles or LUVs), a concentration of detergent and buffer is optimized to balance protein solubility, proteolipid concentration, and LUV stability. Adding detergent also causes the LUVs to partially disassemble and form micelles, which warrants detergent removal to restore LUV integrity. We explore methods of measuring the coexistence of detergent micelles and LUVs to track the different phases of the system as detergent is removed. A combination of Fluorescence Correlation Spectroscopy, Dynamic Light Scattering, and chemical analysis are used to measure the properties of this system. With detergent/LUV number densities as high as 5 we find coexistence of micelles and LUVs at 50% to 60%. As the detergent is removed, the micelle concentration drops to lower than 30% while detergent levels drop to nearly zero. These results may indicate a polydispersed LUV size distribution after detergent mediated reconstitution. Supported by HHMI and Swarthmore College.

  5. Artificial membrane-binding proteins stimulate oxygenation of stem cells during engineering of large cartilage tissue

    NASA Astrophysics Data System (ADS)

    Armstrong, James P. K.; Shakur, Rameen; Horne, Joseph P.; Dickinson, Sally C.; Armstrong, Craig T.; Lau, Katherine; Kadiwala, Juned; Lowe, Robert; Seddon, Annela; Mann, Stephen; Anderson, J. L. Ross; Perriman, Adam W.; Hollander, Anthony P.

    2015-06-01

    Restricted oxygen diffusion can result in central cell necrosis in engineered tissue, a problem that is exacerbated when engineering large tissue constructs for clinical application. Here we show that pre-treating human mesenchymal stem cells (hMSCs) with synthetic membrane-active myoglobin-polymer-surfactant complexes can provide a reservoir of oxygen capable of alleviating necrosis at the centre of hyaline cartilage. This is achieved through the development of a new cell functionalization methodology based on polymer-surfactant conjugation, which allows the delivery of functional proteins to the hMSC membrane. This new approach circumvents the need for cell surface engineering using protein chimerization or genetic transfection, and we demonstrate that the surface-modified hMSCs retain their ability to proliferate and to undergo multilineage differentiation. The functionalization technology is facile, versatile and non-disruptive, and in addition to tissue oxygenation, it should have far-reaching application in a host of tissue engineering and cell-based therapies.

  6. Formulations for modulation of protein release from large-size PLGA microparticles for tissue engineering.

    PubMed

    Qodratnama, Roozbeh; Serino, Lorenzo Pio; Cox, Helen C; Qutachi, Omar; White, Lisa J

    2015-02-01

    In this study we present an approach to pre-program lysozyme release from large size (100-300 μm) poly(DL-lactic acid-co-glycolic acid) (PLGA) microparticles. This approach involved blending in-house synthesized triblock copolymers with a PLGA 85:15. In this work it is demonstrated that the lysozyme release rate and the total release are related to the mass of triblock copolymer present in polymer formulation. Two triblock copolymers (PLGA-PEG1500-PLGA and PLGA-PEG1000-PLGA) were synthesized and used in this study. In a like-for-like comparison, these two triblock copolymers appeared to have similar effects on the release of lysozyme. It was shown that blending resulted in the increase of the total lysozyme release and shortened the release period (70% release within 30 days). These results demonstrated that blending PLGA-PEG-PLGA triblock copolymer with PLGA 85:15 can be used as a method to pre-program protein release from microparticles. These microparticles with modulated protein release properties may be used to create microparticle-based tissue engineering constructs with pre-programmed release properties.

  7. The Large Conductance, Calcium-activated K+ (BK) Channel is regulated by Cysteine String Protein

    PubMed Central

    Kyle, Barry D.; Ahrendt, Eva; Braun, Andrew P.; Braun, Janice E. A.

    2013-01-01

    Large-conductance, calcium-activated-K+ (BK) channels are widely distributed throughout the nervous system, where they regulate action potential duration and firing frequency, along with presynaptic neurotransmitter release. Our recent efforts to identify chaperones that target neuronal ion channels have revealed cysteine string protein (CSPα) as a key regulator of BK channel expression and current density. CSPα is a vesicle-associated protein and mutations in CSPα cause the hereditary neurodegenerative disorder, adult-onset autosomal dominant neuronal ceroid lipofuscinosis (ANCL). CSPα null mice show 2.5 fold higher BK channel expression compared to wild type mice, which is not seen with other neuronal channels (i.e. Cav2.2, Kv1.1 and Kv1.2). Furthermore, mutations in either CSPα's J domain or cysteine string region markedly increase BK expression and current amplitude. We conclude that CSPα acts to regulate BK channel expression, and consequently CSPα-associated changes in BK activity may contribute to the pathogenesis of neurodegenerative disorders, such as ANCL. PMID:23945775

  8. IC 1257: A New Globular Cluster in the Galactic Halo

    NASA Technical Reports Server (NTRS)

    Harris, W. E.; Phelps, R. L.; Madore, B. F.; Pevunova, O.; Skiff, B. A.; Crute, C.; Wilson, B.

    1996-01-01

    New CCD photometry of the faint, compact star cluster IC 1257 (L = 17? = +/- 15?obtained with the Palomar 5m telescope, reveals that it is a highly reddened globular cluster well beyond the Galactic center.

  9. THE ACCRETION OF DWARF GALAXIES AND THEIR GLOBULAR CLUSTER SYSTEMS

    SciTech Connect

    Masters, Craig E.; Ashman, Keith M. E-mail: ashmank@umkc.ed

    2010-12-10

    The question of where the low-metallicity globular clusters in early-type galaxies came from has profound implications for the formation of those galaxies. Our work supports the idea that the metal-poor globular cluster systems of giant early-type galaxies formed in dwarf galaxies that have been subsumed by the giants. To support this hypothesis, two linear relations, one involving globular cluster metallicity versus host galaxy luminosity and one involving metallicity versus velocity dispersion were studied. Tentatively, these relations show that the bright ellipticals do not obey the same trend as the dwarfs, suggesting that the low-metallicity globular clusters did not form within their parent bright ellipticals.

  10. Globular clusters in the halo of M31

    SciTech Connect

    Racine, R. Canada-France-Hawaii Telescope Corp., Kamuela, HI )

    1991-03-01

    The CFHT was used to obtain high-resolution CCD images of 82 cluster candidates in the halo of M31. These data, combined with radial velocities which cover an additional 27 candidates, are used to compile a catalog of 51 bona fide M31 halo globulars. The other candidates are found to be background galaxies (54) and field stars (4). The cluster sample appears to be incomplete for V greater than 18. The projected distribution of globulars follows an 1/r-squared law for r(kpc) between values of 6 and 22 and then drops faster, suggesting a cutoff at about 40 kpc. These trends are similar to those for globular clusters in the Milky Way halo. The total populaton of globulars in M31 is estimated to be larger than in the Milky Way by a factor of 1.8 + or - 0.3. 30 refs.

  11. MUSE crowded field 3D spectroscopy of over 12 000 stars in the globular cluster NGC 6397. I. The first comprehensive HRD of a globular cluster

    NASA Astrophysics Data System (ADS)

    Husser, Tim-Oliver; Kamann, Sebastian; Dreizler, Stefan; Wendt, Martin; Wulff, Nina; Bacon, Roland; Wisotzki, Lutz; Brinchmann, Jarle; Weilbacher, Peter M.; Roth, Martin M.; Monreal-Ibero, Ana

    2016-04-01

    Aims: We demonstrate the high multiplex advantage of crowded field 3D spectroscopy with the new integral field spectrograph MUSE by means of a spectroscopic analysis of more than 12 000 individual stars in the globular cluster NGC 6397. Methods: The stars are deblended with a point spread function fitting technique, using a photometric reference catalogue from HST as prior, including relative positions and brightnesses. This catalogue is also used for a first analysis of the extracted spectra, followed by an automatic in-depth analysis via a full-spectrum fitting method based on a large grid of PHOENIX spectra. Results: We analysed the largest sample so far available for a single globular cluster of 18 932 spectra from 12 307 stars in NGC 6397. We derived a mean radial velocity of vrad = 17.84 ± 0.07 km s-1 and a mean metallicity of [Fe/H] = -2.120 ± 0.002, with the latter seemingly varying with temperature for stars on the red giant branch (RGB). We determine Teff and [Fe/H] from the spectra, and log g from HST photometry. This is the first very comprehensive Hertzsprung-Russell diagram (HRD) for a globular cluster based on the analysis of several thousands of stellar spectra, ranging from the main sequence to the tip of the RGB. Furthermore, two interesting objects were identified; one is a post-AGB star and the other is a possible millisecond-pulsar companion. Data products are available at http://muse-vlt.eu/scienceBased on observations obtained at the Very Large Telescope (VLT) of the European Southern Observatory, Paranal, Chile (ESO Programme ID 60.A-9100(C)).

  12. Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

    PubMed

    Selwa, Edithe; Huynh, Tru; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Thérèse E

    2014-10-01

    The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations.

  13. Early nucleosynthesis and chemical abundances of stars in globular clusters.

    NASA Astrophysics Data System (ADS)

    Gratton, R. G.

    This cycle of lectures presents a self consistent sketch of current understanding about chemcial composition of globular clusters and its aftermaths. The first two lectures give basic about nucleosynthesis, chemical models, and abundance determinations. Main results for globular clusters are presented in the next two lectures. In the final lecture the author reviews various indices used to derive abundances from photometry and low dispersion spectroscopy.

  14. Most Massive Globular Cluster in Our Galaxy

    NASA Astrophysics Data System (ADS)

    1994-05-01

    Far down in the southern sky, in the constellation of Centaurus, a diffuse spot of light can be perceived with the unaided eye. It may be unimpressive, but when seen through a telescope, it turns out to be a beautiful, dense cluster of innumerable stars [1]. Omega Centauri, as this object is called, is the brightest of its type in the sky. We refer to it as a "globular cluster", due to its symmetric form. It belongs to our Milky Way galaxy and astrophysical investigations have shown that it is located at a distance of about 16,500 light-years (1 light-year = 9,460,000,000,000 km). Nobody knows for sure how many individual stars it contains, but recent estimates run into the millions. Most of these stars are more than 10,000 million years old and it is generally agreed that Omega Centauri has a similar age. Measurements of its motion indicate that Omega Centauri plows through the Milky Way in an elongated orbit. It is not easy to understand how it has managed to keep its stars together during such an extended period. MEASURING STELLAR VELOCITIES IN OMEGA CENTAURI A group of astronomers [2] have recently carried through a major investigation of Omega Centauri. After many nights of observations at the ESO La Silla observatory, they now conclude that not only is this globular cluster the brightest, it is indeed by far the most massive known in the Milky Way. The very time-consuming observations were made during numerous observing sessions over a period of no less than 13 years (1981-1993), with the photoelectric spectrometer CORAVEL mounted on the 1.5-m Danish telescope at La Silla. The CORAVEL instrument (COrelation RAdial VELocities) was built in a joint effort between the Geneva (Switzerland) and Marseilles (France) observatories. It functions according to the cross-correlation technique, by means of which the spectrum of the observed star is compared with a "standard stellar spectrum" [3]. HOW HEAVY IS OMEGA CENTAURI? In the present study, a total of 1701

  15. Large molecule protein feeding during the suckling period is required for the development of pancreatic digestive functions in rats.

    PubMed

    Kinouchi, Toshi; Koyama, Satomi; Harada, Etsumori; Yajima, Takaji

    2012-12-15

    We examined if large molecule protein feeding during the suckling period is prerequisite for the proper development of pancreatic digestive functions. Most amino acids in breast milk exist as the constituent of large proteins and not as oligopeptides or free amino acids. Accumulating evidence indicates the nutritional importance of large protein feeding for suckling infants; however, evidence on the physiological significance remains small. We thus artificially reared rat pups on a standard rat formula with milk protein or a formula with milk protein hydrolysate from 7 to 21 days of age, and thereafter, fed a standard solid diet until 42 days of age. Pancreas weight and the stock of pancreatic digestive enzymes in the hydrolysate-fed rats were significantly lower than those in the protein-fed rats during and also after the suckling period. Plasma insulin, a stimulator of amylase synthesis, was also significantly low in the hydrolysate-fed rats compared with the protein-fed rats. At 28 days of age, we evaluated the pancreatic secretory ability in response to dietary protein and cholecystokinin (CCK) by means of pancreatic duct cannulation. Pancreatic secretion stimulated by dietary protein in the hydrolysate-fed rats was significantly weaker than that in the protein-fed rats. No significant difference was observed in the increasing rate of pancreatic enzyme secretion in response to CCK between the two groups. These results suggest that the presence of large proteins in breast milk is significant for the development of pancreatic digestive functions and the outcomes could remain even later on in life.

  16. What Happens to the Gas in Globular Clusters?

    NASA Astrophysics Data System (ADS)

    Thoul, A.; Jehin, E.; Magain, P.; Noels, A.; Parmentier, G.

    Observations of globular clusters show that they contain much too little gas or dust, compared to what should be present due to the mass-losing stars in the cluster. Many authors have been intrigued by the fate of the gas in globular clusters. They have suggested various mechanisms by which the gas could escape from the cluster, such as stellar UV radiation, cluster winds driven by X-ray bursters, novae, or flare-stars, relativistic winds from millisecond pulsars, condensation into stars, accretion processes drawing upon a central gas reservoir, continuous sweeping of the cluster gas by the gaseous medium of the Galactic halo dots. Recent results also show that globular cluster stars show many abundance anomalies. Accretion of interstellar gas by the cluster stars has been suggested as a plausible mechanism to explain these anomalies. It is also a major ingredient of the EASE scenario linking halo field stars to globular clusters, which we have recently developed to explain strong r-and s-elements correlations in halo field dwarf stars. Here we will briefly review the status of gas and dust detection in globular clusters, as well as the possible gas removal mechanisms. We will explore in more details the gas and dust accretion processes onto main sequence stars. In particular, we will study the efficiency of this mechanism in removing gas from the globular clusters interstellar medium.

  17. Sucralose Destabilization of Protein Structure.

    PubMed

    Chen, Lee; Shukla, Nimesh; Cho, Inha; Cohn, Erin; Taylor, Erika A; Othon, Christina M

    2015-04-16

    Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion.

  18. Effect of competing short-range attraction and long-range repulsion on the dynamics of globular particle suspensions

    NASA Astrophysics Data System (ADS)

    Riest, Jonas; Naegele, Gerhard

    2015-03-01

    The dynamic clustering of globular particle suspensions exhibiting competing short-range attraction and long-range repulsion such as protein solutions has gained a lot of interest in the last years. We investigate the influence of clustering on the phase behavior, and in particular on the dynamics of globular particle systems. To this end, we explore various pair potential models by a combination of static and dynamic analytic calculation methods in conjunction with Molecular Dynamics and Monte Carlo simulations. Our results show that the cluster peak (intermediate-range-order peak) is present also in the hydrodynamic function characterizing the short-time dynamics. Moreover, an enhanced short-range attraction leads to a larger sedimentation velocity and a smaller self-diffusion coefficient. Our results are useful also for technical applications, such as in the ultrafiltration of proteins.

  19. STRUCTURAL PARAMETERS FOR GLOBULAR CLUSTERS IN M31

    SciTech Connect

    Wang Song; Ma Jun

    2013-08-01

    In this paper, we present surface brightness profiles for 79 globular clusters in M31, using images observed with the Hubble Space Telescope, some of which are from new observations. The structural and dynamical parameters are derived from fitting the profiles to several different models for the first time. The results show that in the majority of cases, King models fit the M31 clusters just as well as Wilson models and better than Sersic models. However, there are 11 clusters best fitted by Sersic models with the Sersic index n > 2, meaning that they have cuspy central density profiles. These clusters may be the well-known core-collapsed candidates. There is a bimodality in the size distribution of M31 clusters at large radii, which is different from their Galactic counterparts. In general, the properties of clusters in M31 and the Milky Way fall in the same regions of parameter spaces. The tight correlations of cluster properties indicate a ''fundamental plane'' for clusters, which reflects some universal physical conditions and processes operating at the epoch of cluster formation.

  20. The X-Ray Globular Cluster Population in NGC 1399

    NASA Technical Reports Server (NTRS)

    Angelini, Lorella; Loewenstein, Michael; Mushotzky, Richard F.; White, Nicholas E. (Technical Monitor)

    2001-01-01

    We report on X-ray sources detected in the Chandra images of the elliptical galaxy NGC 1399 and identified with globular clusters (GCs). The 8'x 8' Chandra image shows that a large fraction of the 2-10 keV X-ray emission is resolved into point sources, with a luminosity threshold of 5 x 10 (exp 37) ergs s-1. These sources are most likely Low Mass X-ray Binaries (LMXBs). More than 70% of the X-ray sources, in a region imaged by Hubble Space Telescope (HST), are located within GCs. Many of these sources have super-Eddington luminosity (for an accreting neutron star) and their average luminosity is higher than the remaining sources. This association suggests that, in giant elliptical galaxies, luminous X-ray binaries preferentially form in GCs. The spectral properties of the GC and non-GC sources are in most cases similar to those of LMXBs in our galaxy. Two of the brightest sources, one of which is in GC, have a much softer spectra as seen in the high state black hole. The "apparent" super-Eddington luminosity in many cases may be due to multiple LMXB systems within individual GC, but with some of the most extreme luminous systems containing massive black holes.

  1. Probing the faintest stars in a globular star cluster.

    PubMed

    Richer, Harvey B; Anderson, Jay; Brewer, James; Davis, Saul; Fahlman, Gregory G; Hansen, Brad M S; Hurley, Jarrod; Kalirai, Jasonjot S; King, Ivan R; Reitzel, David; Rich, R Michael; Shara, Michael M; Stetson, Peter B

    2006-08-18

    NGC 6397 is the second closest globular star cluster to the Sun. Using 5 days of time on the Hubble Space Telescope, we have constructed an ultradeep color-magnitude diagram for this cluster. We see a clear truncation in each of its two major stellar sequences. Faint red main-sequence stars run out well above our observational limit and near to the theoretical prediction for the lowest mass stars capable of stable hydrogen burning in their cores. We also see a truncation in the number counts of faint blue stars, namely white dwarfs. This reflects the limit to which the bulk of the white dwarfs can cool over the lifetime of the cluster. There is also a turn toward bluer colors in the least luminous of these objects. This was predicted for the very coolest white dwarfs with hydrogen-rich atmospheres as the formation of H(2) and the resultant collision-induced absorption cause their atmospheres to become largely opaque to infrared radiation.

  2. Biophysics of protein evolution and evolutionary protein biophysics

    PubMed Central

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  3. Protein engineering methods applied to membrane protein targets.

    PubMed

    Lluis, M W; Godfroy, J I; Yin, H

    2013-02-01

    Genes encoding membrane proteins have been estimated to comprise as much as 30% of the human genome. Among these membrane, proteins are a large number of signaling receptors, transporters, ion channels and enzymes that are vital to cellular regulation, metabolism and homeostasis. While many membrane proteins are considered high-priority targets for drug design, there is a dearth of structural and biochemical information on them. This lack of information stems from the inherent insolubility and instability of transmembrane domains, which prevents easy obtainment of high-resolution crystals to specifically study structure-function relationships. In part, this lack of structures has greatly impeded our understanding in the field of membrane proteins. One method that can be used to enhance our understanding is directed evolution, a molecular biology method that mimics natural selection to engineer proteins that have specific phenotypes. It is a powerful technique that has considerable success with globular proteins, notably the engineering of protein therapeutics. With respect to transmembrane protein targets, this tool may be underutilized. Another powerful tool to investigate membrane protein structure-function relationships is computational modeling. This review will discuss these protein engineering methods and their tremendous potential in the study of membrane proteins.

  4. istar: A Web Platform for Large-Scale Protein-Ligand Docking

    PubMed Central

    Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J.; Wong, Man-Hon

    2014-01-01

    Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

  5. istar: a web platform for large-scale protein-ligand docking.

    PubMed

    Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J; Wong, Man-Hon

    2014-01-01

    Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

  6. Molecular importance of prawn large heat shock proteins 60, 70 and 90.

    PubMed

    Chaurasia, Mukesh Kumar; Nizam, Faizal; Ravichandran, Gayathri; Arasu, Mariadhas Valan; Al-Dhabi, Naif Abdullah; Arshad, Aziz; Elumalai, Preetham; Arockiaraj, Jesu

    2016-01-01

    Considering the importance of heat shock proteins (HSPs) in the innate immune system of prawn, a comparative molecular approach was proposed to study the crustacean large HSPs 60, 70 and 90. Three different large HSPs were identified from freshwater prawn Macrobrachium rosenbergii (Mr) cDNA library during screening. The structural and functional characteristic features of HSPs were studied using various bioinformatics tools. Also, their gene expression and mRNA regulation upon various pathogenic infections was studied by relative quantification using 2(-ΔΔCT) method. MrHSP60 contains a long chaperonin 60 domain at 46-547 which carries a chaperonin 60 signature motif between 427 and 438, whereas MrHSP70 contains a long HSP70 domain at 21-624 and MrHSP90 carries a HSP90 domain at 188-719. The two dimensional analysis showed that MrHSP60 contains more amino acids (52%) in helices, whereas MrHSP70 (40.6%) and MrHSP90 (51.8%) carried more residues in coils. Gene expression results showed significant (P < 0.05) expression of MrHSP60, 70 and 90 in haemocyte, gill and hepatopancreas, respectively. Further, the expression level was up-regulated upon bacterial (Aeromonas hydrophilla and Vibrio harveyi) and viral [white spot syndrome virus (WSSV) and M. rosenbergii nodo virus (MrNV)] infections during various time periods. The gene expression results exhibited the potential involvement of these three HSPs in the immune system of prawn. The study indicated the potentiality of these molecules, thereby protecting cells against pathogens as well as severe cellular and environmental stresses in crustaceans.

  7. Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins

    NASA Astrophysics Data System (ADS)

    Bondalapati, Somasekhar; Jbara, Muhammad; Brik, Ashraf

    2016-05-01

    Methods to prepare proteins that include a specific modification at a desired position are essential for understanding their cellular functions and physical properties in living systems. Chemical protein synthesis, which relies on the chemoselective ligation of unprotected peptides, enables the preparation of modified proteins that are not easily fabricated by other methods. In contrast to recombinant approaches, chemical synthesis can be used to prepare protein analogues such as D-proteins, which are useful in protein structure determination and the discovery of novel therapeutics. Post-translationally modifying proteins is another example where chemical protein synthesis proved itself as a powerful approach for preparing samples with high homogeneity and in workable quantities. In this Review, we discuss the basic principles of the field, focusing on novel chemoselective peptide ligation approaches such as native chemical ligation and the recent advances based on this method with a proven record of success in the synthesis of highly important protein targets.

  8. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

    NASA Astrophysics Data System (ADS)

    Ciemny, Maciej Pawel; Debinski, Aleksander; Paczkowska, Marta; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

    2016-12-01

    Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure.

  9. HST Snapshot Study of Variable Stars in Globular Clusters: Inner Region of NGC 6441

    NASA Technical Reports Server (NTRS)

    Pritzl, Barton J.; Smith, Horace A.; Stetson, Peter B.; Catelan, Marcio; Sweigart, Allen V.; Layden, Andrew C.; Rich, R. Michael

    2003-01-01

    We present the results of a Hubble Space Telescope snapshot program to survey the inner region of the metal-rich globular cluster NGC 6441 for its variable stars. A total of 57 variable stars was found including 38 RR Lyrae stars, 6 Population II Cepheids, and 12 long period variables. Twenty-four of the RR Lyrae stars and all of the Population II Cepheids were previously undiscovered in ground-based surveys. Of the RR Lyrae stars observed in h s survey, 26 are pulsating in the fundamental mode with a mean period of 0.753 d and 12 are first-overtone mode pulsators with a mean period of 0.365 d. These values match up very well with those found in ground-based surveys. Combining all the available data for NGC 6441, we find mean periods of 0.759 d and 0.375 d for the RRab and RRc stars, respectively. We also find that the RR Lyrae in this survey are located in the same regions of a period-amplitude diagram as those found in ground-based surveys. The overall ratio of RRc to total RR Lyrae is 0.33. Although NGC 6441 is a metal-rich globular cluster and would, on that ground, be expected either to have few RR Lyrae stars, or to be an Oosterhoff type I system, its RR Lyrae more closely resemble those in Oosterhoff type II globular clusters. However, even compared to typical Oosterhoff type II systems, the mean period of its RRab stars is unusually long. We also derived I-band period-luminosity relations for the RR Lyrae stars. Of the six Population II Cepheids, five are of W Virginis type and one is a BL Herculis variable star. This makes NGC 6441, along with NGC 6388, the most metal-rich globular cluster known to contain these types of variable stars. Another variable, V118, may also be a Population II Cepheid given its long period and its separation in magnitude from the RR Lyrae stars. We examine the period-luminosity relation for these Population II Cepheids and compare it to those in other globular clusters and in the Large Magellanic Cloud. We argue that there does

  10. Abundances for globular cluster giants. I. Homogeneous metallicities for 24 clusters

    NASA Astrophysics Data System (ADS)

    Carretta, E.; Gratton, R. G.

    1997-01-01

    We have obtained high resolution, high signal-to-noise ratio CCD echelle spectra of 10 bright red giants in 3 globular clusters (47 Tuc, NGC 6752 and NGC 6397) roughly spanning the whole range of metallicities of the galactic globular cluster system. The analysis of this newly acquired material reveals no significant evidence of star-to-star variation of the [Fe/H] ratio in these three clusters. Moreover, a large set of high quality literature data (equivalent widths from high dispersion CCD spectra) was re-analyzed in an homogeneous and self-consistent way to integrate our observations and derive new metal abundances for more than 160 bright red giants in 24 globular clusters (i.e. about 16% of the known population of galactic globulars). This set was then used to define a new metallicity scale for globular clusters which is the result of high quality, direct spectroscopic data, of new and updated model atmospheres from the grid of \\cite[Kurucz (1992)]{\\ref41}, and of a careful fine abundance analysis; this last, in turn, is based on a common set of both atomic and atmospheric parameters for all the stars examined. Given the very high degree of internal homogeneity, our new scale supersedes the offsets and discrepancies existing in previous attempts to obtain a metallicity scale. The internal uncertainty in [Fe/H] is very small: 0.06 dex (24 clusters) on average, and can be interpreted also as the mean precision of the c luster ranking. Compared to our system, metallicities on the widely used Zinn and West's scale are about 0.10 dex higher for [Fe/H]>-1, 0.23 dex lower for -1<[Fe/H]<-1.9 and 0.11 dex too high for [Fe/H]<-1.9. The non-linearity of the Zinn and West's scale is significant even at 3 sigma level. A quadratic transformation is given to correct older values to the new scale in the range of our calibrating clusters (-2.24 <= [Fe/H]ZW <= -0.51). A minor disagreement is found at low metallicities between the metallicity scale based on field and cluster

  11. Oct4-enhanced green fluorescent protein transgenic pigs: a new large animal model for reprogramming studies.

    PubMed

    Nowak-Imialek, Monika; Kues, Wilfried A; Petersen, Bjoern; Lucas-Hahn, Andrea; Herrmann, Doris; Haridoss, Srividyameena; Oropeza, Marianne; Lemme, Erika; Schöler, Hans R; Carnwath, Joseph W; Niemann, Heiner

    2011-09-01

    The domesticated pig has emerged as an important tool for development of surgical techniques, advancement of xenotransplantation, creation of important disease models, and preclinical testing of novel cell therapies. However, germ line-competent pluripotent porcine stem cells have not yet been derived. This has been a major obstacle to genetic modification of pigs. The transcription factor Oct4 is essential for the maintenance of pluripotency and for reprogramming somatic cells to a pluripotent state. Here, we report the production of transgenic pigs carrying an 18 kb genomic sequence of the murine Oct4 gene fused to the enhanced green fluorescent protein (EGFP) cDNA (OG2 construct) to allow identification of pluripotent cells by monitoring Oct4 expression by EGFP fluorescence. Eleven viable transgenic piglets were produced by somatic cell nuclear transfer. Expression of the EGFP reporter construct was confined to germ line cells, the inner cell mass and trophectoderm of blastocysts, and testicular germ cells. Reprogramming of fibroblasts from these animals by fusion with pluripotent murine embryonic stem cells or viral transduction with human OCT4, SOX2, KLF4, and c-MYC cDNAs resulted in Oct4-EGFP reactivation. The OG2 pigs have thus proved useful for monitoring reprogramming and the induction and maintenance of pluripotency in porcine cells. In conclusion, the OG2 transgenic pigs are a new large animal model for studying the derivation and maintenance of pluripotent cells, and will be valuable for the development of cell therapy.

  12. Analyzing Large-Scale Structural Change in Proteins: Comparison of Principal Component Projection and Sammon Mapping

    SciTech Connect

    Mesentean, Sidonia; Fischer, S.; Smith, Jeremy C

    2006-04-01

    Effective analysis of large-scale conformational transitions in macromolecules requires transforming them into a lower dimensional representation that captures the dominant motions. Herein, we apply and compare two different dimensionality reduction techniques, namely, principal component analysis (PCA), a linear method, and Sammon mapping, which is nonlinear. The two methods are used to analyze four different protein transition pathways of varying complexity, obtained by using either the conjugate peak refinement method or constrained molecular dynamics. For the return-stroke in myosin, both Sammon mapping and PCA show that the conformational change is dominated by a simple rotation of a rigid body. Also, in the case of the T{yields}R transition in hemoglobin, both methods are able to identify the two main quaternary transition events. In contrast, in the cases of the unfolding transition of staphylococcal nuclease or the signaling switch of Ras p21, which are both more complex conformational transitions, only Sammon mapping is able to identify the distinct phases of motion.

  13. Population Models for Massive Globular Clusters

    NASA Astrophysics Data System (ADS)

    Lee, Young-Wook; Joo, Seok-Joo; Han, Sang-Il; Na, Chongsam; Lim, Dongwook; Roh, Dong-Goo

    2015-03-01

    Increasing number of massive globular clusters (GCs) in the Milky Way are now turned out to host multiple stellar populations having different heavy element abundances enriched by supernovae. Recent observations have further shown that [CNO/Fe] is also enhanced in metal-rich subpopulations in most of these GCs, including ω Cen and M22 (Marino et al. 2011, 2012). In order to reflect this in our population modeling, we have expanded the parameter space of Y 2 isochrones and horizontal-branch (HB) evolutionary tracks to include the cases of normal and enhanced nitrogen abundances ([N/Fe] = 0.0, 0.8, and 1.6). The observed variations in the total CNO content were reproduced by interpolating these nitrogen enhanced stellar models. Our test simulations with varying N and O abundances show that, once the total CNO sum ([CNO/Fe]) is held constant, both N and O have almost identical effects on the HR diagram (see Fig. 1).

  14. On eccentricities of globular cluster galactocentric orbits

    NASA Astrophysics Data System (ADS)

    Ninkovic, S.

    The orbital eccentricities of 55 globular clusters are calculated and discussed. The data are taken from the study of Woltjer (1975), but include only those clusters for which reliable chemical compositions, positions, and line-of-sight velocities are given. The clusters are divided into six groups according to chemical composition and galactocentric distance, and the formulas of House and Wiegandt (1977) are employed in the calculations. The results are presented in tables and characterized individually. An LSR velocity of 225 km/sec is assumed, but some calculations using 275 km/sec are included for comparison. A general lower limit of eccentricity of 0.3 and upper limits (depending on cluster type) as high as 0.9 are estimated, with perigalactic distances not less than 1 kpc and apogalactic distances generally less than 25 but sometimes as high as 50-100 kpc. The mean orbital eccentricity of the groups is found to be better correlated to galactocentric distance than to chemical composition. The evolutionary contraction of the Galaxy is estimated to have lasted about 2-3 Gyr.

  15. Large-scale Analysis of Thermo-stable, Mammalian Proteins Provides Insights into the Intrinsically Disordered Proteome

    PubMed Central

    Galea, Charles A.; High, Anthony; Obenauer, John C.; Mishra, Ashutosh; Park, Cheon-Gil; Punta, Marco; Schlessinger, Avner; Ma, Jing; Rost, Burkhard; Slaughter, Clive A.; Kriwacki, Richard W.

    2009-01-01

    Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity to interact with multiple binding partners, disordered proteins are thought to be specialized for roles in signaling and regulation. However, these concepts are based on in silico analyses of translated whole genome sequences, not on large-scale analyses of proteins expressed in living cells. Therefore, whether these concepts broadly apply to expressed proteins is currently unknown. Previous studies have shown that heat-treatment of cell extracts lead to partial enrichment of soluble, disordered proteins. Based on this observation, we sought to address the current dearth of knowledge about expressed, disordered proteins by performing a large-scale proteomics study of thermo-stable proteins isolated from mouse fibroblast cells. Using novel multidimensional chromatography methods and mass spectrometry, we identified a total of 1,320 thermo-stable proteins from these cells. Further, we used a variety of bioinformatics methods to analyze the structural and biological properties of these proteins. Interestingly, more than 900 of these expressed proteins were predicted to be substantially disordered. These were divided into two categories, with 514 predicted to be predominantly disordered and 395 predicted to exhibit both disordered and ordered/folded features. In addition, 411 of the thermo-stable proteins were predicted to be folded. Despite the use of heat treatment (60 min. at 98 °C) to partially enrich for disordered proteins, which might have been expected to select for small proteins, the sequences of these proteins exhibited a wide range of lengths (622 ± 555 residues (average length ± standard deviation) for disordered proteins and 569 ± 598 residues for folded proteins). Computational structural analyses revealed several unexpected features of the thermo

  16. Large-scale identification of putative exported proteins in Candida albicans by genetic selection.

    PubMed

    Monteoliva, L; Matas, M López; Gil, C; Nombela, C; Pla, J

    2002-08-01

    In all living organisms, secreted proteins play essential roles in different processes. Of special interest is the construction of the fungal cell wall, since this structure is absent from mammalian cells. The identification of the proteins involved in its biogenesis is therefore a primary goal in antifungal research. To perform a systematic identification of such proteins in Candida albicans, we carried out a genetic screening in which in-frame fusions with an intracellular allele of invertase gene SUC2 of Saccharomyces cerevisiae can be used to select and identify putatively exported proteins in the heterologous host S. cerevisiae. Eighty-three clones were selected, including 11 previously identified genes from C. albicans as well as 41 C. albicans genes that encode proteins homologous to already described proteins from related organisms. They include enzymes involved in cell wall synthesis and protein secretion. We also found membrane receptors and transporters presumably related to the interaction of C. albicans with the environment as well as extracellular enzymes and proteins involved in different morphological transitions. In addition, 11 C. albicans open reading frames (ORFs) identified in this screening encode proteins homologous to unknown or putative proteins, while 5 ORFs encode novel secreted proteins without known homologues in other organisms. This screening procedure therefore not only identifies a set of targets of interest in antifungal research but also provides new clues for understanding the topological locations of many proteins involved in processes relevant to the pathogenicity of this microorganism.

  17. Large-Scale Identification of Putative Exported Proteins in Candida albicans by Genetic Selection

    PubMed Central

    Monteoliva, L.; López Matas, M.; Gil, C.; Nombela, C.; Pla, J.

    2002-01-01

    In all living organisms, secreted proteins play essential roles in different processes. Of special interest is the construction of the fungal cell wall, since this structure is absent from mammalian cells. The identification of the proteins involved in its biogenesis is therefore a primary goal in antifungal research. To perform a systematic identification of such proteins in Candida albicans, we carried out a genetic screening in which in-frame fusions with an intracellular allele of invertase gene SUC2 of Saccharomyces cerevisiae can be used to select and identify putatively exported proteins in the heterologous host S. cerevisiae. Eighty-three clones were selected, including 11 previously identified genes from C. albicans as well as 41 C. albicans genes that encode proteins homologous to already described proteins from related organisms. They include enzymes involved in cell wall synthesis and protein secretion. We also found membrane receptors and transporters presumably related to the interaction of C. albicans with the environment as well as extracellular enzymes and proteins involved in different morphological transitions. In addition, 11 C. albicans open reading frames (ORFs) identified in this screening encode proteins homologous to unknown or putative proteins, while 5 ORFs encode novel secreted proteins without known homologues in other organisms. This screening procedure therefore not only identifies a set of targets of interest in antifungal research but also provides new clues for understanding the topological locations of many proteins involved in processes relevant to the pathogenicity of this microorganism. PMID:12456000

  18. Galactic globular cluster 47 Tucanae: new ties between the chemical and dynamical evolution of globular clusters?

    NASA Astrophysics Data System (ADS)

    Kučinskas, A.; Dobrovolskas, V.; Bonifacio, P.

    2014-08-01

    Context. It is generally accepted today that Galactic globular clusters (GGCs) consist of at least two generations of stars that are different in their chemical composition and perhaps age. However, knowledge about the kinematical properties of these stellar generations, which may provide important information for constraining evolutionary scenarios of the GGCs, is still limited. Aims: We study the connections between chemical and kinematical properties of different stellar generations in the Galactic globular cluster 47 Tuc. Methods: To achieve this goal, we used abundances of Li, O, and Na determined in 101 main sequence turn-off (TO) stars with the aid of 3D hydrodynamical model atmospheres and NLTE abundance analysis methodology. We divided our sample TO stars into three groups according to their position in the [Li/Na] - [Na/O] plane to study their spatial distribution and kinematical properties. Results: We find that there are statistically significant radial dependencies of lithium and oxygen abundances, A(Li) and A(O), as well as that of [Li/Na] abundance ratio. Our results show that first-generation stars are less centrally concentrated and dynamically hotter than stars belonging to subsequent generations. We also find a significant correlation between the velocity dispersion and O and Na abundance, and between the velocity dispersion and the [Na/O] abundance ratio.

  19. Debottlenecking recombinant protein production in Bacillus megaterium under large-scale conditions--targeted precursor feeding designed from metabolomics.

    PubMed

    Korneli, Claudia; Bolten, Christoph Josef; Godard, Thibault; Franco-Lara, Ezequiel; Wittmann, Christoph

    2012-06-01

    In the present work the impact of large production scale was investigated for Bacillus megaterium expressing green fluorescent protein (GFP). Specifically designed scale-down studies, mimicking the intermittent and continuous nutrient supply of large- and small-scale processes, were carried out for this purpose. The recombinant strain revealed a 40% reduced GFP yield for the large-scale conditions. In line with extended carbon loss via formation of acetate and carbon dioxide, this indicated obvious limitations in the underlying metabolism of B. megaterium under the large-scale conditions. Quantitative analysis of intracellular amino acids via validated fast filtration protocols revealed that their level strongly differed between the two scenarios. During cultivation in large-scale set-up, the availability of most amino acids, serving as key building blocks of the recombinant protein, was substantially reduced. This was most pronounced for tryptophan, aspartate, histidine, glutamine, and lysine. In contrast alanine was increased, probably related to a bottleneck at the level of pyruvate which also triggered acetate overflow metabolism. The pre-cursor quantifications could then be exploited to verify the presumed bottlenecks and improve recombinant protein production under large-scale conditions. Addition of only 5 mM tryptophan, aspartate, histidine, glutamine, and lysine to the feed solution increased the GFP yield by 100%. This rational concept of driving the lab scale productivity of recombinant microorganisms under suboptimal feeding conditions emulating large scale can easily be extended to other processes and production hosts.

  20. Large oncosomes contain distinct protein cargo and represent a separate functional class of tumor-derived extracellular vesicles.

    PubMed

    Minciacchi, Valentina R; You, Sungyong; Spinelli, Cristiana; Morley, Samantha; Zandian, Mandana; Aspuria, Paul-Joseph; Cavallini, Lorenzo; Ciardiello, Chiara; Reis Sobreiro, Mariana; Morello, Matteo; Kharmate, Geetanjali; Jang, Su Chul; Kim, Dae-Kyum; Hosseini-Beheshti, Elham; Tomlinson Guns, Emma; Gleave, Martin; Gho, Yong Song; Mathivanan, Suresh; Yang, Wei; Freeman, Michael R; Di Vizio, Dolores

    2015-05-10

    Large oncosomes (LO) are atypically large (1-10 µm diameter) cancer-derived extracellular vesicles (EVs), originating from the shedding of membrane blebs and associated with advanced disease. We report that 25% of the proteins, identified by a quantitative proteomics analysis, are differentially represented in large and nano-sized EVs from prostate cancer cells. Proteins enriched in large EVs included enzymes involved in glucose, glutamine and amino acid metabolism, all metabolic processes relevant to cancer. Glutamine metabolism was altered in cancer cells exposed to large EVs, an effect that was not observed upon treatment with exosomes. Large EVs exhibited discrete buoyant densities in iodixanol (OptiPrep(TM)) gradients. Fluorescent microscopy of large EVs revealed an appearance consistent with LO morphology, indicating that these structures can be categorized as LO. Among the proteins enriched in LO, cytokeratin 18 (CK18) was one of the most abundant (within the top 5th percentile) and was used to develop an assay to detect LO in the circulation and tissues of mice and patients with prostate cancer. These observations indicate that LO represent a discrete EV type that may play a distinct role in tumor progression and that may be a source of cancer-specific markers.

  1. Ultraviolet properties of individual hot stars in globular cluster cores. 1: NGC 1904 (M 79)

    NASA Technical Reports Server (NTRS)

    Altner, Bruce; Matilsky, Terry A.

    1992-01-01

    As part of an observing program using the International Ultraviolet Explorer (IUE) satellite to investigate the ultraviolet properties of stars found within the cores of galactic globular clusters with blue horizontal branches (HBs), we obtained three spectra of the cluster NGC 1904 (M 79). All three were long integration-time, short-wavelength (SWP) spectra obtained at the so called 'center of light' and all three showed evidence of sources within the IUE large aperture (21.4 in. by 10 in.). In this paper we shall describe the analysis of these spectra and present evidence that the UV sources represent individual hot stars in the post-HB stage of evolution.

  2. An expression vector taolored for large-scale, high-throughput purification of recombinant proteins.

    SciTech Connect

    Donnelly, M.; Zhou, M.; Sanville Millard, C.; Clancy, S.; Stols, L.; Eschenfeldt, W.; Collart, F.; Joachimiak, A.; Biosciences Division

    2006-01-01

    Production of milligram quantities of numerous proteins for structural and functional studies requires an efficient purification pipeline. We found that the dual tag, his(6)-tag-maltose-binding protein (MBP), intended to facilitate purification and enhance proteins' solubility, disrupted such a pipeline, requiring additional screening and purification steps. Not all proteins rendered soluble by fusion to MBP remained soluble after its proteolytic removal, and in those cases where the protein remained soluble, standard purification protocols failed to remove completely the stoichiometric amount of his(6)-tagged MBP generated by proteolysis. Both liabilities were alleviated by construction of a vector that produces fusion proteins in which MBP, the his(6)-tag and the target protein are separated by highly specific protease cleavage sites in the configuration MBP-site-his(6)-site-protein. In vivo cleavage at the first site by co-expressed protease generated untagged MBP and his(6)-tagged target protein. Proteins not truly rendered soluble by transient association with MBP precipitated, and untagged MBP was easily separated from the his-tagged target protein by conventional protocols. The second protease cleavage site allowed removal of the his(6)-tag.

  3. Tidal Stripping of Globular Clusters in a Simulated Galaxy Cluster

    NASA Astrophysics Data System (ADS)

    Ramos, F.; Coenda, V.; Muriel, H.; Abadi, M.

    2015-06-01

    Using a cosmological N-body numerical simulation of the formation of a galaxy-cluster-sized halo, we analyze the temporal evolution of its globular cluster population. We follow the dynamical evolution of 38 galactic dark matter halos orbiting in a galaxy cluster that at redshift z = 0 has a virial mass of 1.71 × 1014 M⊙ h-1. In order to mimic both “blue” and “red” populations of globular clusters, for each galactic halo we select two different sets of particles at high redshift (z ≈ 1), constrained by the condition that, at redshift z = 0, their average radial density profiles are similar to the observed profiles. As expected, the general galaxy cluster tidal field removes a significant fraction of the globular cluster populations to feed the intracluster population. On average, halos lost approximately 16% and 29% of their initial red and blue globular cluster populations, respectively. Our results suggest that these fractions strongly depend on the orbital trajectory of the galactic halo, specifically on the number of orbits and on the minimum pericentric distance to the galaxy cluster center that the halo has had. At a given time, these fractions also depend on the current clustercentric distance, just as observations show that the specific frequency of globular clusters SN depends on their clustercentric distance.

  4. Enrichment by supernovae in globular clusters with multiple populations.

    PubMed

    Lee, Jae-Woo; Kang, Young-Woon; Lee, Jina; Lee, Young-Wook

    2009-11-26

    The most massive globular cluster in the Milky Way, omega Centauri, is thought to be the remaining core of a disrupted dwarf galaxy, as expected within the model of hierarchical merging. It contains several stellar populations having different heavy elemental abundances supplied by supernovae-a process known as metal enrichment. Although M 22 appears to be similar to omega Cen, other peculiar globular clusters do not. Therefore omega Cen and M 22 are viewed as exceptional, and the presence of chemical inhomogeneities in other clusters is seen as 'pollution' from the intermediate-mass asymptotic-giant-branch stars expected in normal globular clusters. Here we report Ca abundances for seven globular clusters and compare them to omega Cen. Calcium and other heavy elements can only be supplied through numerous supernovae explosions of massive stars in these stellar systems, but the gravitational potentials of the present-day clusters cannot preserve most of the ejecta from such explosions. We conclude that these globular clusters, like omega Cen, are most probably the relics of more massive primeval dwarf galaxies that merged and disrupted to form the proto-Galaxy.

  5. TIDAL STRIPPING OF GLOBULAR CLUSTERS IN A SIMULATED GALAXY CLUSTER

    SciTech Connect

    Ramos, F.; Coenda, V.; Muriel, H.; Abadi, M.

    2015-06-20

    Using a cosmological N-body numerical simulation of the formation of a galaxy-cluster-sized halo, we analyze the temporal evolution of its globular cluster population. We follow the dynamical evolution of 38 galactic dark matter halos orbiting in a galaxy cluster that at redshift z = 0 has a virial mass of 1.71 × 10{sup 14} M{sub ⊙} h{sup −1}. In order to mimic both “blue” and “red” populations of globular clusters, for each galactic halo we select two different sets of particles at high redshift (z ≈ 1), constrained by the condition that, at redshift z = 0, their average radial density profiles are similar to the observed profiles. As expected, the general galaxy cluster tidal field removes a significant fraction of the globular cluster populations to feed the intracluster population. On average, halos lost approximately 16% and 29% of their initial red and blue globular cluster populations, respectively. Our results suggest that these fractions strongly depend on the orbital trajectory of the galactic halo, specifically on the number of orbits and on the minimum pericentric distance to the galaxy cluster center that the halo has had. At a given time, these fractions also depend on the current clustercentric distance, just as observations show that the specific frequency of globular clusters S{sub N} depends on their clustercentric distance.

  6. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    PubMed Central

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. PMID:25774711

  7. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins.

    PubMed

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J; Weik, Martin

    2015-03-16

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  8. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    NASA Astrophysics Data System (ADS)

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-03-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  9. Effects of Spontaneous Heating on Forage Protein Fractions and In Situ Disappearance Kinetics of Crude Protein for Alfalfa-Orchardgrass Hays Packaged in Large-Round Bales

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During 2006 and 2007, forages from 3 individual hay harvests were utilized to assess the effects of spontaneous heating on concentrations of crude protein (CP), neutral-detergent insoluble CP (NDICP), acid-detergent insoluble CP (ADICP), and in situ disappearance kinetics of CP and NDICP for large-r...

  10. Influence of fermentable carbohydrates or protein on large intestinal and urinary metabolomic profiles in piglets.

    PubMed

    Pieper, R; Neumann, K; Kröger, S; Richter, J F; Wang, J; Martin, L; Bindelle, J; Htoo, J K; Vahjen, V; Van Kessel, A G; Zentek, J

    2012-12-01

    It was recently shown that variations in the ratio of dietary fermentable carbohydrates (fCHO) and fermentable protein (fCP) differentially affect large intestinal microbial ecology and the mucosal response. Here we investigated the use of mass spectrometry to profile changes in metabolite composition in colon and urine associated with variation in dietary fCHO and fCP composition and mucosal physiology. Thirty-two weaned piglets were fed 4 diets in a 2 × 2 factorial design with low fCP and low fCHO, low fCP and high fCHO, high fCP and low fCHO, and high fCP and high fCHO. After 21 to 23 d, all pigs were euthanized and colon digesta and urine metabolite profiles were obtained by mass spectrometry. Analysis of mass spectra by partial least squares approach indicated a clustering of both colonic and urinary profiles for each pig by feeding group. Metabolite identification and annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed increased abundance of metabolites associated with arachidonic acid metabolism in colon of pigs fed a high concentration of fCP irrespective of dietary fCHO. Urinary metabolites did not show as clear patterns. Mass spectrometry can effectively differentiate metabolite profiles in colon contents and urine associated with changes in dietary composition. Whether metabolite profiling is an effective tool to identify specific metabolites (biomarkers) or metabolite profiles associated with gut function and integrity needs further elucidation.

  11. Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases

    PubMed Central

    2012-01-01

    Background Gene duplications have been proposed to be the main mechanism involved in genome evolution and in acquisition of new functions. Polydnaviruses (PDVs), symbiotic viruses associated with parasitoid wasps, are ideal model systems to study mechanisms of gene duplications given that PDV genomes consist of virulence genes organized into multigene families. In these systems the viral genome is integrated in a wasp chromosome as a provirus and virus particles containing circular double-stranded DNA are injected into the parasitoids’ hosts and are essential for parasitism success. The viral virulence factors, organized in gene families, are required collectively to induce host immune suppression and developmental arrest. The gene family which encodes protein tyrosine phosphatases (PTPs) has undergone spectacular expansion in several PDV genomes with up to 42 genes. Results Here, we present strong indications that PTP gene family expansion occurred via classical mechanisms: by duplication of large segments of the chromosomally integrated form of the virus sequences (segmental duplication), by tandem duplications within this form and by dispersed duplications. We also propose a novel duplication mechanism specific to PDVs that involves viral circle reintegration into the wasp genome. The PTP copies produced were shown to undergo conservative evolution along with episodes of adaptive evolution. In particular recently produced copies have undergone positive selection in sites most likely involved in defining substrate selectivity. Conclusion The results provide evidence about the dynamic nature of polydnavirus proviral genomes. Classical and PDV-specific duplication mechanisms have been involved in the production of new gene copies. Selection pressures associated with antagonistic interactions with parasitized hosts have shaped these genes used to manipulate lepidopteran physiology with evidence for positive selection involved in adaptation to host targets. PMID

  12. Globular Clusters Indicate That Ultra-diffuse Galaxies Are Dwarfs

    NASA Astrophysics Data System (ADS)

    Beasley, Michael A.; Trujillo, Ignacio

    2016-10-01

    We present an analysis of archival HST/ACS imaging in the F475W (g 475), F606W (V 606), and F814W (I 814) bands of the globular cluster (GC) system of a large (3.4 kpc effective radius) ultra-diffuse galaxy (DF17) believed to be located in the Coma Cluster of galaxies. We detect 11 GCs down to the 5σ completeness limit of the imaging (I 814 = 27 mag). Correcting for background and our detection limits yields a total population of GCs in this galaxy of 27 ± 5 and a V-band specific frequency S N = 28 ± 5. Based on comparisons to the GC systems of local galaxies, we show that both the absolute number and the colors of the GC system of DF17 are consistent with the GC system of a dark-matter-dominated dwarf galaxy with virial mass ˜9.0 × 1010 M ⊙ and a dark-to-stellar mass ratio M vir/M star ˜ 1000. Based on the stellar mass growth of the Milky Way, we show that DF17 cannot be understood as a failed Milky-Way-like system, but is more similar to quenched Large-Magellanic-Cloud-like systems. We find that the mean color of the GC population, g 475-I 814 = 0.91 ± 0.05 mag, coincides with the peak of the color distribution of intracluster GCs and is also similar to those of the blue GCs in the outer regions of massive galaxies. We suggest that both the intracluster GC population in Coma and the blue peak in the GC populations of massive galaxies may be fed—at least in part—by the disrupted equivalents of systems such as DF17.

  13. THE DYNAMICAL EVOLUTION OF STELLAR BLACK HOLES IN GLOBULAR CLUSTERS

    SciTech Connect

    Morscher, Meagan; Pattabiraman, Bharath; Rodriguez, Carl; Rasio, Frederic A.; Umbreit, Stefan

    2015-02-10

    Our current understanding of the stellar initial mass function and massive star evolution suggests that young globular clusters (GCs) may have formed hundreds to thousands of stellar-mass black holes (BHs), the remnants of stars with initial masses from ∼20-100 M {sub ☉}. Birth kicks from supernova explosions may eject some BHs from their birth clusters, but most should be retained. Using a Monte Carlo method we investigate the long-term dynamical evolution of GCs containing large numbers of stellar BHs. We describe numerical results for 42 models, covering a broad range of realistic initial conditions, including up to 1.6 × 10{sup 6} stars. In almost all models we find that significant numbers of BHs (up to ∼10{sup 3}) are retained all the way to the present. This is in contrast to previous theoretical expectations that most BHs should be ejected dynamically within a few gigayears The main reason for this difference is that core collapse driven by BHs (through the Spitzer {sup m}ass segregation instability{sup )} is easily reverted through three-body processes, and involves only a small number of the most massive BHs, while lower-mass BHs remain well-mixed with ordinary stars far from the central cusp. Thus the rapid segregation of stellar BHs does not lead to a long-term physical separation of most BHs into a dynamically decoupled inner core, as often assumed previously. Combined with the recent detections of several BH X-ray binary candidates in Galactic GCs, our results suggest that stellar BHs could still be present in large numbers in many GCs today, and that they may play a significant role in shaping the long-term dynamical evolution and the present-day dynamical structure of many clusters.

  14. Disruption of the Globular Cluster Pal 5

    NASA Technical Reports Server (NTRS)

    Miller, R. H.; Smith, B. F.; Cuzzi, Jeffrey N. (Technical Monitor)

    1995-01-01

    Orbit calculations suggest that the sparse globular cluster, Pal 5, will pass within 7 kpc of the Galactic center the next time it crosses the plane, where it might be destroyed by tidal stresses. We study this problem, treating Pal 5 as a self-consistent dynamical system orbiting through an external potential that represents the Galaxy. The first part of the problem is to find suitable analytic approximations to the Galactic potential. They must be valid in all regions the cluster is likely to explore. Observed velocity and positional data for Pal 5 are used as initial conditions to determine the orbit. Methods we used for a different problem some 12 years ago have been adapted to this problem. Three experiments have been run, with M/L= 1, 3, and 10, for the cluster model. The cluster blew up shortly after passing through the Galactic plane (about 130 Myrs after the beginning of the run) with M/L=1. At M/L = 3 and 10 the cluster survived, although it got quite a kick in the fundamental mode on passing through the plane. But the fundamental mode oscillation died out in a couple of oscillation cycles at M/L=10. Pal 5 will probably be destroyed on its next crossing of the Galactic plane if M/L=1, but it can survive (albeit with fairly heavy damage) if NI/L=3. We haven't tried to trap the mass limits more closely than that. Pal 5 comes through pretty well unscathed at M/L=10. An interesting follow-up experiment would be to back the cluster up along its orbit to look at its previous passage through the Galactic plane, to see what kind of object it might have been at earlier times.

  15. THE TIMING OF NINE GLOBULAR CLUSTER PULSARS

    SciTech Connect

    Lynch, Ryan S.; Freire, Paulo C. C.; Ransom, Scott M.; Jacoby, Bryan A. E-mail: pfreire@mpifr-bonn.mpg.de E-mail: bryan.jacoby@gmail.com

    2012-02-01

    We have used the Robert C. Byrd Green Bank Telescope to time nine previously known pulsars without published timing solutions in the globular clusters (GCs) M62, NGC 6544, and NGC 6624. We have full timing solutions that measure the spin, astrometric, and (where applicable) binary parameters for six of these pulsars. The remaining three pulsars (reported here for the first time) were not detected enough to establish solutions. We also report our timing solutions for five pulsars with previously published solutions, and find good agreement with other authors, except for PSR J1701-3006B in M62. Gas in this system is probably responsible for the discrepancy in orbital parameters, and we have been able to measure a change in the orbital period over the course of our observations. Among the pulsars with new solutions we find several binary pulsars with very low mass companions (members of the so-called 'black widow' class) and we are able to place constraints on the mass-to-light ratio in two clusters. We confirm that one of the pulsars in NGC 6624 is indeed a member of the rare class of non-recycled pulsars found in GCs. We have also measured the orbital precession and Shapiro delay for a relativistic binary in NGC 6544. If we assume that the orbital precession can be described entirely by general relativity, which is likely, we are able to measure the total system mass (2.57190(73) M{sub Sun }) and companion mass (1.2064(20) M{sub Sun }), from which we derive the orbital inclination (sin i = 0.9956(14)) and the pulsar mass (1.3655(21) M{sub Sun }), the most precise such measurement ever obtained for a millisecond pulsar. The companion is the most massive known around a fully recycled pulsar.

  16. YOUNG RADIO PULSARS IN GALACTIC GLOBULAR CLUSTERS

    SciTech Connect

    Boyles, J.; Lorimer, D. R.; Turk, P. J.; Mnatsakanov, R.; Lynch, R. S.; Ransom, S. M.; Freire, P. C.; Belczynski, K.

    2011-11-20

    Currently three isolated radio pulsars and one binary radio pulsar with no evidence of any previous recycling are known in 97 surveyed Galactic globular clusters (GCs). As pointed out by Lyne et al., the presence of these pulsars cannot be explained by core-collapse supernovae, as commonly assumed for their counterparts in the Galactic disk. We apply a Bayesian analysis to the results from surveys for radio pulsars in GCs and find the number of potentially observable non-recycled radio pulsars present in all clusters to be <3600. Accounting for beaming and retention considerations, the implied birthrate for any formation scenario for all 97 clusters is <0.25 pulsars century{sup -1} assuming a Maxwellian distribution of velocities with a dispersion of 10 km s{sup -1}. The implied birthrates for higher velocity dispersions are substantially higher than inferred for such pulsars in the Galactic disk. This suggests that the velocity dispersion of young pulsars in GCs is significantly lower than those of disk pulsars. These numbers may be substantial overestimates due to the fact that the currently known sample of young pulsars is observed only in metal-rich clusters. We propose that young pulsars may only be formed in GCs with metallicities with log[Fe/H] > - 0.6. In this case, the potentially observable population of such young pulsars is 447{sup +1420}{sub -399} (the error bars give a 95% confidence interval) and their birthrate is 0.012{sup +0.037}{sub -0.010} pulsars century{sup -1}. The most likely creation scenario to explain these pulsars is the electron capture supernova of an OMgNe white dwarf.

  17. Large-scale identification of adverse drug reaction-related proteins through a random walk model

    PubMed Central

    Chen, Xiaowen; Shi, Hongbo; Yang, Feng; Yang, Lei; Lv, Yingli; Wang, Shuyuan; Dai, Enyu; Sun, Dianjun; Jiang, Wei

    2016-01-01

    Adverse drug reactions (ADRs) are responsible for drug failure in clinical trials and affect life quality of patients. The identification of ADRs during the early phases of drug development is an important task. Therefore, predicting potential protein targets eliciting ADRs is essential for understanding the pathogenesis of ADRs. In this study, we proposed a computational algorithm,Integrated Network for Protein-ADR relations (INPADR), to infer potential protein-ADR relations based on an integrated network. First, the integrated network was constructed by connecting the protein-protein interaction network and the ADR similarity network using known protein-ADR relations. Then, candidate protein-ADR relations were further prioritized by performing a random walk with restart on this integrated network. Leave-one-out cross validation was used to evaluate the ability of the INPADR. An AUC of 0.8486 was obtained, which was a significant improvement compared to previous methods. We also applied the INPADR to two ADRs to evaluate its accuracy. The results suggested that the INPADR is capable of finding novel protein-ADR relations. This study provides new insight to our understanding of ADRs. The predicted ADR-related proteins will provide a reference for preclinical safety pharmacology studies and facilitate the identification of ADRs during the early phases of drug development. PMID:27805066

  18. [Electron transfer between globular proteins. Evaluation of a matrix element].

    PubMed

    Lakhno, V D; Chuev, G N; Ustinin, M N

    1998-01-01

    The dependence of the matrix element of the probability of interprotein electron transfer on the mutual orientation of the donor and acceptor centers and the distance between them was calculated. The calculations were made under the assumption that electron transfer proceeds mainly by a collective excitation of polaron nature, like a solvated electron state. The results obtained are consistent with experimental data and indicate the nonexponential behavior of this dependence in the case when the distance transfer is less than 20 A.

  19. Estimation of Sedimentation Coefficients and Frictional Ratios of Globular Proteins.

    ERIC Educational Resources Information Center

    Smith, Christopher A.

    1988-01-01

    Describes a program to support lectures on analytical centrifugation, and to illustrate the manner in which useful analytical data about macromolecules can be obtained from simple centrifugation studies without the need for mathematical expertise. Discusses the background, methods, calculations, and results involved in this activity. (CW)

  20. Astronomers Ponder Lack of Planets in Globular Cluster

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This videotape has seven segments, discussing and showing the evidence for the proposition that the galactic clusters do not have many planets. Specifically the segments show: (1) Dr. Ron Gilliland discussing the process of looking for "Hot Jupiters" (i.e., planets about the size of Jupiter, which are hotter than Jupiter) in the globular clusters, (2) a zoom into 47 Tucanae globular cluster, (3) an animation of a planet passing between the host star and the earth with a brightness graph, (4) the same animation as before without the graph, (5) Ron Gilliland of the Space Telescope Science Institute (STScI) discussing possible interpretations of his findings in the 47 Tucanae globular cluster, (6) Ron Gilliland examining the images of 47 Tucanae, and (7) images of 47 Tucanae watching for variations in brightness.

  1. Pulsar-irradiated stars in dense globular clusters

    NASA Technical Reports Server (NTRS)

    Tavani, Marco

    1992-01-01

    We discuss the properties of stars irradiated by millisecond pulsars in 'hard' binaries of dense globular clusters. Irradiation by a relativistic pulsar wind as in the case of the eclipsing millisecond pulsar PSR 1957+20 alter both the magnitude and color of the companion star. Some of the blue stragglers (BSs) recently discovered in dense globular clusters can be irradiated stars in binaries containing powerful millisecond pulsars. The discovery of pulsar-driven orbital modulations of BS brightness and color with periods of a few hours together with evidence for radio and/or gamma-ray emission from BS binaries would valuably contribute to the understanding of the evolution of collapsed stars in globular clusters. Pulsar-driven optical modulation of cluster stars might be the only observable effect of a new class of binary pulsars, i.e., hidden millisecond pulsars enshrouded in the evaporated material lifted off from the irradiated companion star.

  2. Latent dynamics of a protein molecule observed in dihedral angle space

    NASA Astrophysics Data System (ADS)

    Omori, Satoshi; Fuchigami, Sotaro; Ikeguchi, Mitsunori; Kidera, Akinori

    2010-03-01

    Dihedral angles are alternative set of variables to Cartesian coordinates for representing protein dynamics. The two sets of variables exhibit extremely different behavior. Motions in dihedral angle space are characterized by latent dynamics, in which motion induced in each dihedral angle is always compensated for by motions of many other dihedral angles, in order to maintain a rigid globular shape. Using molecular dynamics simulations, we propose a molecular mechanism for the latent dynamics in dihedral angle space. It was found that, due to the unique structure of dihedral principal components originating in the globular shape of the protein, the dihedral principal components with large (small) amplitudes are highly correlated with the eigenvectors of the metric matrix with small (large) eigenvalues. Such an anticorrelation in the eigenmode structures minimizes the mean square displacement of Cartesian coordinates upon rotation of dihedral angles. In contrast, a short peptide, deca-alanine in this study, does not show such behavior of the latent dynamics in the dihedral principal components, but shows similar behaviors to those of the Cartesian principal components, due to the absence of constraints to maintain a rigid globular shape.

  3. Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles

    PubMed Central

    Deeb, Sally J.; Tyanova, Stefka; Hummel, Michael; Schmidt-Supprian, Marc; Cox, Juergen; Mann, Matthias

    2015-01-01

    Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but this requires accurate and robust tools. Here, we develop a state of the art quantitative mass spectrometric pipeline to characterize formalin-fixed paraffin-embedded tissues of patients with closely related subtypes of diffuse large B-cell lymphoma. We combined a super-SILAC approach with label-free quantification (hybrid LFQ) to address situations where the protein is absent in the super-SILAC standard but present in the patient samples. Shotgun proteomic analysis on a quadrupole Orbitrap quantified almost 9,000 tumor proteins in 20 patients. The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origin using both their global protein expression patterns and the 55-protein signature obtained previously from patient-derived cell lines (Deeb, S. J., D'Souza, R. C., Cox, J., Schmidt-Supprian, M., and Mann, M. (2012) Mol. Cell. Proteomics 11, 77–89). Expression levels of individual segregation-driving proteins as well as categories such as extracellular matrix proteins behaved consistently with known trends between the subtypes. We used machine learning (support vector machines) to extract candidate proteins with the highest segregating power. A panel of four proteins (PALD1, MME, TNFAIP8, and TBC1D4) is predicted to classify patients with low error rates. Highly ranked proteins from the support vector analysis revealed differential expression of core signaling molecules between the subtypes, elucidating aspects of their pathobiology. PMID:26311899

  4. Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles.

    PubMed

    Deeb, Sally J; Tyanova, Stefka; Hummel, Michael; Schmidt-Supprian, Marc; Cox, Juergen; Mann, Matthias

    2015-11-01

    Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but this requires accurate and robust tools. Here, we develop a state of the art quantitative mass spectrometric pipeline to characterize formalin-fixed paraffin-embedded tissues of patients with closely related subtypes of diffuse large B-cell lymphoma. We combined a super-SILAC approach with label-free quantification (hybrid LFQ) to address situations where the protein is absent in the super-SILAC standard but present in the patient samples. Shotgun proteomic analysis on a quadrupole Orbitrap quantified almost 9,000 tumor proteins in 20 patients. The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origin using both their global protein expression patterns and the 55-protein signature obtained previously from patient-derived cell lines (Deeb, S. J., D'Souza, R. C., Cox, J., Schmidt-Supprian, M., and Mann, M. (2012) Mol. Cell. Proteomics 11, 77-89). Expression levels of individual segregation-driving proteins as well as categories such as extracellular matrix proteins behaved consistently with known trends between the subtypes. We used machine learning (support vector machines) to extract candidate proteins with the highest segregating power. A panel of four proteins (PALD1, MME, TNFAIP8, and TBC1D4) is predicted to classify patients with low error rates. Highly ranked proteins from the support vector analysis revealed differential expression of core signaling molecules between the subtypes, elucidating aspects of their pathobiology.

  5. Chemical Compositions of Stars in Globular Cluster NGC 2419

    NASA Astrophysics Data System (ADS)

    Kadakia, Shimonee; Smecker-Hane, T.; Bosler, T.

    2007-05-01

    We determine the chemical abundances of 19 red giant branch stars in the Galactic globular cluster NGC 2419. Lying at a distance of 84.2 kpc and a galactocentric distance of 91.5 kpc, NGC 2419 is the fourth brightest globular cluster in the Milky Way with a total magnitude of M_V = -9.6 mag, which is significantly brighter than M_V = -7.5 mag, the typical peak of the globular cluster luminosity functions in external galaxies. Our results will give an insight of whether NGC 2419 is in fact a globular cluster or a core of a disrupted galaxy that merged with the Milky Way. We have used IRAF to reduce spectra we have taken with the DEIMOS spectrograph on the the Keck I 10-meter telescope. Using the strengths of the Ca II triplet absorption lines at approximately 8600 Angstrom, we will determine the chemical abundance of each star. If the chemical abundances differ by significantly more than the observational errors would predict then we can conclude the cluster is a remnant of the core of a galaxy that merged with the Milky Way and not a normal globular cluster, because most globular clusters formed quickly from a well mixed gas cloud, and thus their stars have nearly identical ages and chemical compositions. We gratefully acknowledge financial support from a UROP grant to SK and NSF grant AST-0307863 to TSH. These data were obtained at the Keck Observatory, operated by the California Inst. of Technology, Univ. of California and NASA and made possible by generous financial support from the W.M. Keck Foundation.

  6. A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction

    NASA Astrophysics Data System (ADS)

    Johnson, J.; Brackley, C. A.; Cook, P. R.; Marenduzzo, D.

    2015-02-01

    We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.

  7. A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction.

    PubMed

    Johnson, J; Brackley, C A; Cook, P R; Marenduzzo, D

    2015-02-18

    We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.

  8. Support Vector Machines Trained with Evolutionary Algorithms Employing Kernel Adatron for Large Scale Classification of Protein Structures

    PubMed Central

    Arana-Daniel, Nancy; Gallegos, Alberto A.; López-Franco, Carlos; Alanís, Alma Y.; Morales, Jacob; López-Franco, Adriana

    2016-01-01

    With the increasing power of computers, the amount of data that can be processed in small periods of time has grown exponentially, as has the importance of classifying large-scale data efficiently. Support vector machines have shown good results classifying large amounts of high-dimensional data, such as data generated by protein structure prediction, spam recognition, medical diagnosis, optical character recognition and text classification, etc. Most state of the art approaches for large-scale learning use traditional optimization methods, such as quadratic programming or gradient descent, which makes the use of evolutionary algorithms for training support vector machines an area to be explored. The present paper proposes an approach that is simple to implement based on evolutionary algorithms and Kernel-Adatron for solving large-scale classification problems, focusing on protein structure prediction. The functional properties of proteins depend upon their three-dimensional structures. Knowing the structures of proteins is crucial for biology and can lead to improvements in areas such as medicine, agriculture and biofuels. PMID:27980384

  9. Support Vector Machines Trained with Evolutionary Algorithms Employing Kernel Adatron for Large Scale Classification of Protein Structures.

    PubMed

    Arana-Daniel, Nancy; Gallegos, Alberto A; López-Franco, Carlos; Alanís, Alma Y; Morales, Jacob; López-Franco, Adriana

    2016-01-01

    With the increasing power of computers, the amount of data that can be processed in small periods of time has grown exponentially, as has the importance of classifying large-scale data efficiently. Support vector machines have shown good results classifying large amounts of high-dimensional data, such as data generated by protein structure prediction, spam recognition, medical diagnosis, optical character recognition and text classification, etc. Most state of the art approaches for large-scale learning use traditional optimization methods, such as quadratic programming or gradient descent, which makes the use of evolutionary algorithms for training support vector machines an area to be explored. The present paper proposes an approach that is simple to implement based on evolutionary algorithms and Kernel-Adatron for solving large-scale classification problems, focusing on protein structure prediction. The functional properties of proteins depend upon their three-dimensional structures. Knowing the structures of proteins is crucial for biology and can lead to improvements in areas such as medicine, agriculture and biofuels.

  10. On the importance of polar interactions for complexes containing intrinsically disordered proteins.

    PubMed

    Wong, Eric T C; Na, Dokyun; Gsponer, Jörg

    2013-01-01

    There is a growing recognition for the importance of proteins with large intrinsically disordered (ID) segments in cell signaling and regulation. ID segments in these proteins often harbor regions that mediate molecular recognition. Coupled folding and binding of the recognition regions has been proposed to confer high specificity to interactions involving ID segments. However, researchers recently questioned the origin of the interaction specificity of ID proteins because of the overrepresentation of hydrophobic residues in their interaction interfaces. Here, we focused on the role of polar and charged residues in interactions mediated by ID segments. Making use of the extended nature of most ID segments when in complex with globular proteins, we first identified large numbers of complexes between globular proteins and ID segments by using radius-of-gyration-based selection criteria. Consistent with previous studies, we found the interfaces of these complexes to be enriched in hydrophobic residues, and that these residues contribute significantly to the stability of the interaction interface. However, our analyses also show that polar interactions play a larger role in these complexes than in structured protein complexes. Computational alanine scanning and salt-bridge analysis indicate that interfaces in ID complexes are highly complementary with respect to electrostatics, more so than interfaces of globular proteins. Follow-up calculations of the electrostatic contributions to the free energy of binding uncovered significantly stronger Coulombic interactions in complexes harbouring ID segments than in structured protein complexes. However, they are counter-balanced by even higher polar-desolvation penalties. We propose that polar interactions are a key contributing factor to the observed high specificity of ID segment-mediated interactions.

  11. A large dataset of protein dynamics in the mammalian heart proteome

    PubMed Central

    Lau, Edward; Cao, Quan; Ng, Dominic C.M.; Bleakley, Brian J.; Dincer, T. Umut; Bot, Brian M.; Wang, Ding; Liem, David A.; Lam, Maggie P.Y.; Ge, Junbo; Ping, Peipei

    2016-01-01

    Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems. PMID:26977904

  12. The J-domain proteins of Arabidopsis thaliana: an unexpectedly large and diverse family of chaperones.

    PubMed

    Miernyk, J A

    2001-07-01

    A total of 89 J-domain proteins were identified in the genome of the model flowering plant Arabidopsis thaliana. The deduced amino acid sequences of the J-domain proteins were analyzed for an assortment of structural features and motifs. Based on the results of sequence comparisons and structure and function predictions, 51 distinct families were identified. The families ranged in size from 1 to 6 members. Subcellular localizations of the A thaliana J-domain proteins were predicted; species were found in both the soluble and membrane compartments of all cellular organelles. Based on digital Northern analysis, the J-domain proteins could be separated into groups of low, medium, and moderate expression levels. This genomics-based analysis of the A thaliana J-domain proteins establishes a framework for detailed studies of biological function and specificity. It additionally provides a comprehensive basis for evolutionary comparisons.

  13. Sistemas de cúmulos globulares extragalácticos

    NASA Astrophysics Data System (ADS)

    Forte, J. C.

    Se describen las características de los sistemas de cúmulos globulares asociados a galaxias elípticas en una variedad de medios y, en particular, aquellas vinculadas con la distribución espacial, frecuencia específica y composición química. Esta discusión se hace dentro de un conjunto de esquemas orientados a explicar las primeras fases de la formación de las galaxias dominantes en cúmulos y del rol de los sistemas de cúmulos globulares en esos procesos.

  14. Fukuyoa paulensis gen. et sp. nov., a new genus for the globular species of the dinoflagellate Gambierdiscus (Dinophyceae).

    PubMed

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi/G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov.

  15. Fukuyoa paulensis gen. et sp. nov., a New Genus for the Globular Species of the Dinoflagellate Gambierdiscus (Dinophyceae)

    PubMed Central

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M.; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi / G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov. PMID:25831082

  16. Robotic large-scale application of wheat cell-free translation to structural studies including membrane proteins

    PubMed Central

    Beebe, Emily T.; Makino, Shin-ichi; Nozawa, Akira; Matsubara, Yuko; Frederick, Ronnie O.; Primm, John G.; Goren, Michael A.; Fox, Brian G.

    2010-01-01

    The use of the Protemist XE, an automated discontinuous-batch protein synthesis robot, in cell-free translation is reported. The soluble Galdieria sulphuraria protein DCN1 was obtained in greater than 2 mg total synthesis yield per mL of reaction mixture from the Protemist XE, and the structure was subsequently solved by X-ray crystallography using material from one 10 mL synthesis (PDB ID: 3KEV). The Protemist XE was also capable of membrane protein translation. Thus human sigma-1 receptor was translated in the presence of unilamellar liposomes and bacteriorhodopsin was translated directly into detergent micelles in the presence of all-trans-retinal. The versatility, ease of use, and compact size of the Protemist XE robot demonstrate its suitability for large-scale synthesis of many classes of proteins. PMID:20637905

  17. Maize (Zea mays)-derived bovine trypsin: characterization of the first large-scale, commercial protein product from transgenic plants.

    PubMed

    Woodard, Susan L; Mayor, Jocelyne M; Bailey, Michele R; Barker, Donna K; Love, Robert T; Lane, Jeffrey R; Delaney, Donna E; McComas-Wagner, Janet M; Mallubhotla, Hanuman D; Hood, Elizabeth E; Dangott, Lawrence J; Tichy, Shane E; Howard, John A

    2003-10-01

    Bovine trypsin (EC 3.4.21.4) is an enzyme that is widely used for commercial purposes to digest or process other proteins, including some therapeutic proteins. The biopharmaceutical industry is trying to eliminate animal-derived proteins from manufacturing processes due to the possible contamination of these products by human pathogens. Recombinant trypsin has been produced in a number of systems, including cell culture, bacteria and yeast. To date, these expression systems have not produced trypsin on a scale sufficient to fulfill the need of biopharmaceutical manufacturers where kilogram quantities are often required. The present paper describes commercial-level production of trypsin in transgenic maize (Zea mays) and its physical and functional characterization. This protease, the first enzyme to be produced on a large-scale using transgenic plant technology, is functionally equivalent to native bovine pancreatic trypsin. The availability of this reagent should allow for the replacement of animal-derived trypsin in the processing of pharmaceutical proteins.

  18. Host proteins that bind to or mimic SV40 large T antigen: using antibodies to look at protein interactions and their significance

    PubMed Central

    Mole, S. E.; Gannon, J. V.; Anton, I. A.; Ford, M. J.; Lane, D. P.

    1989-01-01

    The papovavirus SV40 is able to induce tumours in susceptible hosts and will transform cells in vitro. Its major early protein, large T antigen, is required for viral DNA synthesis, both in vivo and in vitro, and is also responsible for the oncogenic action of the virus. We have made use of an extensive library of anti-T monoclonal antibodies to investigate the cellular effects of T. Large T shares an antigenic determinant with a growth-regulated host protein, p68, which is a member of an expanding super-family of helicases with particular homology to the translation initiation factor elF-4A. We have also studied the binding and interaction of large T with two particular host components: the replicative enzyme DNA polymerase α and the proto-oncogene p53. These two proteins bind to similar regions of T and exert similar effects on its antigenic structure. We found that p53 can block the binding of DNA polymerase α to T as well as co-existing with DNA polymerase α in a trimeric complex with T. This suggests that these interactions may be important in the oncogenic and replicative action of large T.

  19. Exploring Symmetry as an Avenue to the Computational Design of Large Protein Domains

    SciTech Connect

    Fortenberry, Carie; Bowman, Elizabeth Anne; Proffitt, Will; Dorr, Brent; Combs, Steven; Harp, Joel; Mizoue, Laura; Meiler, Jens

    2012-03-15

    It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements - 'symmetric superfolds'. Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric ({beta}{alpha}){sub 8} TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.

  20. Large-scale identification of human protein function using topological features of interaction network

    PubMed Central

    Li, Zhanchao; Liu, Zhiqing; Zhong, Wenqian; Huang, Menghua; Wu, Na; Xie, Yun; Dai, Zong; Zou, Xiaoyong

    2016-01-01

    The annotation of protein function is a vital step to elucidate the essence of life at a molecular level, and it is also meritorious in biomedical and pharmaceutical industry. Developments of sequencing technology result in constant expansion of the gap between the number of the known sequences and their functions. Therefore, it is indispensable to develop a computational method for the annotation of protein function. Herein, a novel method is proposed to identify protein function based on the weighted human protein-protein interaction network and graph theory. The network topology features with local and global information are presented to characterise proteins. The minimum redundancy maximum relevance algorithm is used to select 227 optimized feature subsets and support vector machine technique is utilized to build the prediction models. The performance of current method is assessed through 10-fold cross-validation test, and the range of accuracies is from 67.63% to 100%. Comparing with other annotation methods, the proposed way possesses a 50% improvement in the predictive accuracy. Generally, such network topology features provide insights into the relationship between protein functions and network architectures. The source code of Matlab is freely available on request from the authors. PMID:27849060

  1. Exploring symmetry as an avenue to the computational design of large protein domains.

    PubMed

    Fortenberry, Carie; Bowman, Elizabeth Anne; Proffitt, Will; Dorr, Brent; Combs, Steven; Harp, Joel; Mizoue, Laura; Meiler, Jens

    2011-11-16

    It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements--"symmetric superfolds". Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric (βα)(8) TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.

  2. Large-scale identification of human protein function using topological features of interaction network

    NASA Astrophysics Data System (ADS)

    Li, Zhanchao; Liu, Zhiqing; Zhong, Wenqian; Huang, Menghua; Wu, Na; Xie, Yun; Dai, Zong; Zou, Xiaoyong

    2016-11-01

    The annotation of protein function is a vital step to elucidate the essence of life at a molecular level, and it is also meritorious in biomedical and pharmaceutical industry. Developments of sequencing technology result in constant expansion of the gap between the number of the known sequences and their functions. Therefore, it is indispensable to develop a computational method for the annotation of protein function. Herein, a novel method is proposed to identify protein function based on the weighted human protein-protein interaction network and graph theory. The network topology features with local and global information are presented to characterise proteins. The minimum redundancy maximum relevance algorithm is used to select 227 optimized feature subsets and support vector machine technique is utilized to build the prediction models. The performance of current method is assessed through 10-fold cross-validation test, and the range of accuracies is from 67.63% to 100%. Comparing with other annotation methods, the proposed way possesses a 50% improvement in the predictive accuracy. Generally, such network topology features provide insights into the relationship between protein functions and network architectures. The source code of Matlab is freely available on request from the authors.

  3. Far-ultraviolet photometry of the globular cluster omega Cen

    NASA Technical Reports Server (NTRS)

    Whitney, Jonathan H.; O'Connell, Robert W.; Rood, Robert T.; Dorman, Ben; Landsman, Wayne B.; Cheng, K.-P.; Bohlin, Ralph C.; Hintzen, Paul M. N.; Roberts, Morton S.; Smith, Andrew M.

    1994-01-01

    We present far-ultraviolet images of the globular cluster omega Centauri obtained with the Ultraviolet Imaging Telescope (UIT) during the 1990 December Astro-1 mission. A total of 1957 sources are detected at 1620 A to a limiting ultraviolet (UV) magnitude of 16.4 in the central 24 min diameter region of the field and a limit of 15.6 over the remainder of the 40 min diameter field. Over 1400 of these sources are matched with stars on a Stroemgren u band charge coupled devices (CCD) frame obtained with the Cerro Tololo Inter-American Observatory (CTIO) 0.9 m telescope to produce a (far-UV, u) color-magnitude diagram (CMD). Completeness of the sample and error estimates are determined by photometry of artificial stars added to the images. The horizontal branch (HB) of the CMD is heavily populated hotter than 9000 K. A large number of 'extreme HB' stars are found hotter than a conspicuous break in the HB at T(sub e) approximately 16000 K. There is also a significant population of stars above the HB, the brightest of which is 4 mag brighter than the HB. Most of the hotter of these appear to be 'AGB-manque' or 'Post-Early Asymptotic Giant Branch' stars. We compare the observations to recent theoretical evolutionary tracks for the zero-age HB and subsequent phases. The tracks match the data well, with the exception of the hotter HB stars, many of which fall below the zero-age horizontal branch. It is unclear as yet whether these are a special population or an artifact of errors in the models or photometry. We identify 33 stars with T(sub e) greater than or approximately = 50000 K, which are hotter than zero-age HB stars with envelope masses of 0.003 solar mass.

  4. STELLAR COLLISIONS AND BLUE STRAGGLER STARS IN DENSE GLOBULAR CLUSTERS

    SciTech Connect

    Chatterjee, Sourav; Rasio, Frederic A.; Sills, Alison; Glebbeek, Evert

    2013-11-10

    Blue straggler stars (BSSs) are abundantly observed in all Galactic globular clusters (GGCs) where data exist. However, observations alone cannot reveal the relative importance of various formation channels or the typical formation times for this well-studied population of anomalous stars. Using a state-of-the-art Hénon-type Monte Carlo code that includes all relevant physical processes, we create 128 models with properties typical of the observed GGCs. These models include realistic numbers of single and binary stars, use observationally motivated initial conditions, and span large ranges in central density, concentration, binary fraction, and mass. Their properties can be directly compared with those of observed GGCs. We can easily identify the BSSs in our models and determine their formation channels and birth times. We find that for central densities above ∼10{sup 3} M{sub ☉} pc{sup –3}, the dominant formation channel is stellar collisions, while for lower density clusters, mass transfer in binaries provides a significant contribution (up to 60% in our models). The majority of these collisions are binary-mediated, occurring during three-body and four-body interactions. As a result, a strong correlation between the specific frequency of BSSs and the binary fraction in a cluster can be seen in our models. We find that the number of BSSs in the core shows only a weak correlation with the collision rate estimator Γ traditionally used by observers, in agreement with the latest Hubble Space Telescope Advanced Camera for Surveys data. Using an idealized 'full mixing' prescription for collision products, our models indicate that the BSSs observed today may have formed several Gyr ago. However, denser clusters tend to have younger (∼1 Gyr) BSSs.

  5. Photometric and kinematic studies of extragalactic globular cluster systems

    NASA Astrophysics Data System (ADS)

    Dowell, Jessica

    Globular clusters (GCs) are old, luminous, compact collections of stars found in galaxy halos that formed during the early stages of galaxy formation. Because of this, GCs serve as excellent tracers of the formation, structure, and merger history of their host galaxies. My dissertation will examine both the photometric and kinematic properties of GC systems and their relationship to their host galaxies. In the first section, I will present the analysis of the GC systems of two spiral galaxies, NGC 891 and NGC 1055. I will discuss the photometric methods used to detect GCs using wide-field BVR imaging and to quantify the global properties of the system such as the total number of GCs and their radial distribution. My results for these two GC systems were compared to those of other galaxies. I will also present the results of spectroscopic follow-up for two giant galaxies: the S0 galaxy NGC 4594 (M104), and the elliptical galaxy NGC 3379 (M105). I measured the radial velocities of GCs in these two galaxies, and combined them with published results to determine the mass distribution and mass-to-light (M/L) ratio profile for each galaxy out to large effective radius (7-9 Re). For both galaxies, I found that the M/L profiles increase with radius and do not flatten, which suggests that the dark matter halos in these galaxies extend to the edge of my data. I also looked for evidence of rotation in the GC systems, and found that neither system exhibits significant rotation around the host galaxy. I examined the velocity dispersion profile of each GC system and found kinematic differences between the red and blue GC subpopulations. Finally, I compared my results to mass estimates for these galaxies from other kinematic tracers and considered them in the context of galaxy formation models.

  6. Globular Cluster Systems in Brightest Cluster Galaxies. III: Beyond Bimodality

    NASA Astrophysics Data System (ADS)

    Harris, William E.; Ciccone, Stephanie M.; Eadie, Gwendolyn M.; Gnedin, Oleg Y.; Geisler, Douglas; Rothberg, Barry; Bailin, Jeremy

    2017-01-01

    We present new deep photometry of the rich globular cluster (GC) systems around the Brightest Cluster Galaxies UGC 9799 (Abell 2052) and UGC 10143 (Abell 2147), obtained with the Hubble Space Telescope (HST) ACS and WFC3 cameras. For comparison, we also present new reductions of similar HST/ACS data for the Coma supergiants NGC 4874 and 4889. All four of these galaxies have huge cluster populations (to the radial limits of our data, comprising from 12,000 to 23,000 clusters per galaxy). The metallicity distribution functions (MDFs) of the GCs can still be matched by a bimodal-Gaussian form where the metal-rich and metal-poor modes are separated by ≃ 0.8 dex, but the internal dispersions of each mode are so large that the total MDF becomes very broad and nearly continuous from [Fe/H] ≃ ‑2.4 to solar. There are, however, significant differences between galaxies in the relative numbers of metal-rich clusters, suggesting that they underwent significantly different histories of mergers with massive gas-rich halos. Last, the proportion of metal-poor GCs rises especially rapidly outside projected radii R≳ 4 {R}{eff}, suggesting the importance of accreted dwarf satellites in the outer halo. Comprehensive models for the formation of GCs as part of the hierarchical formation of their parent galaxies will be needed to trace the systematic change in structure of the MDF with galaxy mass, from the distinctly bimodal form in smaller galaxies up to the broad continuum that we see in the very largest systems.

  7. Stellar Collisions and Blue Straggler Stars in Dense Globular Clusters

    NASA Astrophysics Data System (ADS)

    Chatterjee, Sourav; Rasio, Frederic A.; Sills, Alison; Glebbeek, Evert

    2013-11-01

    Blue straggler stars (BSSs) are abundantly observed in all Galactic globular clusters (GGCs) where data exist. However, observations alone cannot reveal the relative importance of various formation channels or the typical formation times for this well-studied population of anomalous stars. Using a state-of-the-art Hénon-type Monte Carlo code that includes all relevant physical processes, we create 128 models with properties typical of the observed GGCs. These models include realistic numbers of single and binary stars, use observationally motivated initial conditions, and span large ranges in central density, concentration, binary fraction, and mass. Their properties can be directly compared with those of observed GGCs. We can easily identify the BSSs in our models and determine their formation channels and birth times. We find that for central densities above ~103 M ⊙ pc-3, the dominant formation channel is stellar collisions, while for lower density clusters, mass transfer in binaries provides a significant contribution (up to 60% in our models). The majority of these collisions are binary-mediated, occurring during three-body and four-body interactions. As a result, a strong correlation between the specific frequency of BSSs and the binary fraction in a cluster can be seen in our models. We find that the number of BSSs in the core shows only a weak correlation with the collision rate estimator Γ traditionally used by observers, in agreement with the latest Hubble Space Telescope Advanced Camera for Surveys data. Using an idealized "full mixing" prescription for collision products, our models indicate that the BSSs observed today may have formed several Gyr ago. However, denser clusters tend to have younger (~1 Gyr) BSSs.

  8. Abundances in Globular Cluster Red Giant Stars

    NASA Astrophysics Data System (ADS)

    Cavallo, R. M.

    1997-12-01

    Observations of globular cluster red giant branch (RGB) stars have shown star-to-star variations in the abundances of C, N, O, Na, Mg, and Al, contrary to predictions of standard stellar evolutionary theory. I have modeled the variations in the abundance profiles around the hydrogen-burning shell (H shell) of metal-poor red giant stars by combining four RGB stellar evolutionary sequences of different metallicities with a detailed nuclear reaction network. This approach has significant advantages over previous research: (1) it allows for the variation in the temperature and density around the H shell; (2) it follows the effects of the changing H-shell structure as the sequence evolves; (3) it accounts for the effect of the metallicity on the abundance profiles; (4) it allows the reaction rates to be varied so that their uncertainties may be explored. The results are in good qualitative agreement with the observations. All the models show a region above the H shell in which first C, then O, is depleted in the CN and ON nuclear burning cycles. Within the C-depleted region, the (12) C/(13) C ratio is reduced to its equilibrium value. Just above the O-depleted region, Na is enhanced from proton captures on (22) Ne. In brighter models, Na becomes greatly enhanced within the O-depleted region as the NeNa cycle converts (20) Ne into (23) Na before attaining equilibrium inside the H shell. The more metal-poor models also show Al being increased around the H shell, first from (25,26) Mg, then from (24) Mg in the MgAl cycle. Despite the diminution (24) Mg suffers in synthesizing Al, the models show its abundance is increased due to the NeNa-cycle breakout reaction, (23) Na(p,γ)(24) Mg. This latter result is at odds with observations that show (24) Mg is depleted in a sample of M 13 and NGC 6752 giants (Shetrone 1996, 1997).

  9. A Large-Scale Quantitative Proteomic Approach to Identifying Sulfur Mustard-Induced Protein Phosphorylation Cascades

    DTIC Science & Technology

    2010-01-01

    SILAC method employs 12C14N- and 13C15N-labeled amino acids added directly to the culture medium, resulting in isotopically “light” and “ heavy ” cell...populations, respectively. Protein samples collected from control (light-labeled) and experimental ( heavy -labeled) cells can then be mixed in equal...ratios, digested with trypsin, and analyzed by high-resolution mass spectrometry. The corresponding light and heavy peptides from the same protein will

  10. GeMS MCAO observations of the Galactic globular cluster NGC 2808: the absolute age

    NASA Astrophysics Data System (ADS)

    Massari, D.; Fiorentino, G.; McConnachie, A.; Bono, G.; Dall'Ora, M.; Ferraro, I.; Iannicola, G.; Stetson, P. B.; Turri, P.; Tolstoy, E.

    2016-02-01

    Context. Globular clusters are the oldest stellar systems in the Milky Way, and they probe the early epoch of the Galaxy formation. However, the uncertainties on their absolute age are still too large to soundly constrain how the Galactic structures have assembled. Aims: The aim of this work is to obtain an accurate estimate of the absolute age of the globular cluster NGC 2808 using deep IR data obtained with the multi-conjugate adaptive optics system operating at the Gemini South telescope (GeMS). Methods: This exquisite photometry, combined with that obtained in V and I-bands with HST, allowed us to detect the faint Main Sequence Knee feature in NGC 2808 colour magnitude diagram. The difference between this point and the main sequence turn-off is a good age estimator that provides ages with unprecedented accuracy. Results: We find that NGC 2808 has an age of t = 10.9 ± 0.7 (intrinsic) ±0.45 (metallicity term) Gyr. A possible contamination by He-enhanced population could make the cluster up to 0.25 Gyr older. Although this age estimate agrees with the age coming from the classical turn-off method (t = 11.0 Gyr), its uncertainty is a factor ~3 better, since it avoids systematics in reddening, distance assumptions, and photometric zero point determination. The final absolute age indicates that NGC 2808 is slightly younger than other Galactic globular clusters with similar metallicity. Tables of the photometry are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/586/A51

  11. Heavy elements in globular clusters: The role of asymptotic giant branch stars

    SciTech Connect

    Straniero, O.; Cristallo, S.; Piersanti, L.

    2014-04-10

    Recent observations of heavy elements in globular clusters reveal intriguing deviations from the standard paradigm of the early galactic nucleosynthesis. If the r-process contamination is a common feature of halo stars, s-process enhancements are found in a few globular clusters only. We show that the combined pollution of asymptotic giant branch (AGB) stars with a mass ranging between 3 to 6 M {sub ☉} may account for most of the features of the s-process overabundance in M4 and M22. In these stars, the s process is a mixture of two very different neutron-capture nucleosynthesis episodes. The first is due to the {sup 13}C(α, n){sup 16}O reaction and takes place during the interpulse periods. The second is due to the {sup 22}Ne(α, n){sup 25}Mg reaction and takes place in the convective zones generated by thermal pulses. The production of the heaviest s elements (from Ba to Pb) requires the first neutron burst, while the second produces large overabundances of light s (Rb, Sr, Y, Zr). The first mainly operates in the less massive AGB stars, while the second dominates in the more massive. From the heavy-s/light-s ratio, we derive that the pollution phase should last for 150 ± 50 Myr, a period short enough compared to the formation timescale of the globular cluster system, but long enough to explain why the s-process pollution is observed in a few cases only. With few exceptions, our theoretical prediction provides a reasonable reproduction of the observed s-process abundances, from Sr to Hf. However, Ce is probably underproduced by our models, while Rb and Pb are overproduced. Possible solutions are discussed.

  12. Bayesian Mass Estimates of the Milky Way: Inferring the Mass Profile from Globular Cluster Kinematics

    NASA Astrophysics Data System (ADS)

    Eadie, Gwendolyn; Harris, William E.; Springford, Aaron; Widrow, Larry

    2017-01-01

    The mass and cumulative mass profile of the Milky Way's dark matter halo is a fundamental property of the Galaxy, and yet these quantities remain poorly constrained and span almost two orders of magnitude in the literature. There are a variety of methods to measure the mass of the Milky Way, and a common way to constrain the mass uses kinematic information of satellite objects (e.g. globular clusters) orbiting the Galaxy. One reason precise estimates of the mass and mass profile remain elusive is that the kinematic data of the globular clusters are incomplete; for some both line-of-sight and proper motion measurements are available (i.e. complete data), and for others there are only line-of-sight velocities (i.e. incomplete data). Furthermore, some proper motion measurements suffer from large measurement uncertainties, and these uncertainties can be difficult to take into account because they propagate in complicated ways. Past methods have dealt with incomplete data by using either only the line-of-sight measurements (and throwing away the proper motions), or only using the complete data. In either case, valuable information is not included in the analysis. During my PhD research, I have been developing a coherent hierarchical Bayesian method to estimate the mass and mass profile of the Galaxy that 1) includes both complete and incomplete kinematic data simultaneously in the analysis, and 2) includes measurement uncertainties in a meaningful way. In this presentation, I will introduce our approach in a way that is accessible and clear, and will also present our estimates of the Milky Way's total mass and mass profile using all available kinematic data from the globular cluster population of the Galaxy.

  13. Joint associations of blood plasma proteins with overwinter survival of a large mammal.

    PubMed

    Garnier, Romain; Cheung, Christopher K; Watt, Kathryn A; Pilkington, Jill G; Pemberton, Josephine M; Graham, Andrea L

    2017-02-01

    In many wild animal populations, hosts are at risk of parasites and malnutrition and resource costs of defence may be difficult to afford. We postulate that proteins, important in homeostasis and immunity, play a complex but central role in condition dependence and resource costs of mammalian immune defence. To test this, we measured plasma concentrations of albumin, total proteins. Self-reactive antibodies and parasite-specific IgG in female Soay sheep. Using a principal component analysis, we found a new metric of condition reflecting individual variation in acquisition, assimilation and/or recycling of plasma proteins that predicted overwinter survival. Controlling for this metric, an age-dependent trade-off between antibody titres and protein reserves emerged, indicating costs of mounting an antibody response: younger individuals survived best when prioritising immunity while older individuals fared better when maintaining high-protein nutritional plane. These findings suggest fascinating roles for protein acquisition and allocation in influencing survival in wild animal populations.

  14. THE ORIGIN OF THE SPURIOUS IRON SPREAD IN THE GLOBULAR CLUSTER NGC 3201

    SciTech Connect

    Mucciarelli, A.; Lapenna, E.; Massari, D.; Ferraro, F. R.; Lanzoni, B.

    2015-03-01

    NGC 3201 is a globular cluster suspected to have an intrinsic spread in the iron content. We re-analyzed a sample of 21 cluster stars observed with UVES-FLAMES at the Very Large Telescope and for which Simmerer et al. found a 0.4 dex wide [Fe/H] distribution with a metal-poor tail. We confirmed that when spectroscopic gravities are adopted, the derived [Fe/H] distribution spans ∼0.4 dex. On the other hand, when photometric gravities are used, the metallicity distribution from Fe I lines remains large, while that derived from Fe II lines is narrow and compatible with no iron spread. We demonstrate that the metal-poor component claimed by Simmerer et al. is composed by asymptotic giant branch stars that could be affected by non-local thermodynamical equilibrium effects driven by iron overionization. This leads to a decrease of the Fe I abundance, while leaving the Fe II abundance unaltered. A similar finding has been already found in asymptotic giant branch stars of the globular clusters M5 and 47 Tucanae. We conclude that NGC 3201 is a normal cluster, with no evidence of intrinsic iron spread.

  15. Highly efficient immunodiagnosis of Large cardamom chirke virus using the polyclonal antiserum against Escherichia coli expressed recombinant coat protein.

    PubMed

    Vijayanandraj, S; Yogita, M; Das, Amrita; Ghosh, Amalendu; Mandal, Bikash

    2013-09-01

    Large cardamom chirke virus (LCCV), genus Macluravirus, family Potyviridae is an important constrain in large cardamom production in India. Purification of LCCV from large cardamom tissues is difficult and therefore immunodiagnostic reagents are not available. In the present study, we have successfully expressed coat protein (CP) gene of LCCV in Escherichia coli. The purification of expressed protein by Ni-NTA affinity chromatography was inefficient due to precipitation of protein during renaturation. We have optimized a simple, inexpensive and efficient method for purification of the expressed CP through gel extraction with 5 % SDS followed by renaturation in Milli-Q water, which resulted in high yield (4.7 mg/ml) and good quality of the protein. A higher titer (1:256,000) polyclonal antibody (PAb) to the recombinant CP was produced, which strongly recognized LCCV in crude leaf extract and showed minimal background reaction with the healthy leaf extract in enzyme linked immunosorbent assay (ELISA) and dot immunobinding assay (DIBA). The sensitivities of the ELISA and DIBA were 5 and 0.1 ng of expressed protein, respectively. Both the ELISA and DIBA were validated with 100 % accuracy in detecting LCCV in field samples. The PAb differentiated Cardamom mosaic virus, another close relative of LCCV. Our study is first to report highly efficient immunodiagnosis with PAb to E. coli expressed recombinant CP of a virus under the genus Macluravirus. The antigen expression construct and PAb developed in the present study will be useful in production of virus free planting materials of large cardamom.

  16. Mobility shift detection of phosphorylation on large proteins using a Phos-tag SDS-PAGE gel strengthened with agarose.

    PubMed

    Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Ujihara, Hiromi; Koike, Tohru

    2009-08-01

    We describe a novel technique of phosphate-affinity SDS-PAGE using Phos-tag to analyze large phosphoproteins with molecular masses of more than 200 kDa. The protein phosphoisotypes were clearly separated as up-shifted migration bands in a 3% w/v polyacrylamide gel containing 20 microM Phos-tag and 0.5% w/v agarose. In subsequent immunoblotting, the procedure permitted the determination of the phosphoisotypes of high-molecular-mass proteins, such as mTOR (289 kDa), ATM kinase (350 kDa), and 53BP1 (213 kDa).

  17. Drug Transporters and Na+/H+ Exchange Regulatory Factor PSD-95/Drosophila Discs Large/ZO-1 Proteins

    PubMed Central

    Walsh, Dustin R.; Nolin, Thomas D.

    2015-01-01

    Drug transporters govern the absorption, distribution, and elimination of pharmacologically active compounds. Members of the solute carrier and ATP binding-cassette drug transporter family mediate cellular drug uptake and efflux processes, thereby coordinating the vectorial movement of drugs across epithelial barriers. To exert their physiologic and pharmacological function in polarized epithelia, drug transporters must be targeted and stabilized to appropriate regions of the cell membrane (i.e., apical versus basolateral). Despite the critical importance of drug transporter membrane targeting, the mechanisms that underlie these processes are largely unknown. Several clinically significant drug transporters possess a recognition sequence that binds to PSD-95/Drosophila discs large/ZO-1 (PDZ) proteins. PDZ proteins, such as the Na+/H+ exchanger regulatory factor (NHERF) family, act to stabilize and organize membrane targeting of multiple transmembrane proteins, including many clinically relevant drug transporters. These PDZ proteins are normally abundant at apical membranes, where they tether membrane-delimited transporters. NHERF expression is particularly high at the apical membrane in polarized tissue such as intestinal, hepatic, and renal epithelia, tissues important to drug disposition. Several recent studies have highlighted NHERF proteins as determinants of drug transporter function secondary to their role in controlling membrane abundance and localization. Mounting evidence strongly suggests that NHERF proteins may have clinically significant roles in pharmacokinetics and pharmacodynamics of several pharmacologically active compounds and may affect drug action in cancer and chronic kidney disease. For these reasons, NHERF proteins represent a novel class of post-translational mediators of drug transport and novel targets for new drug development. PMID:26092975

  18. Structural and Dynamical Properties of 29 Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Sohn, Young-Jong; Chun, Mun-Suk; Yim, Hong-Suh; Byun, Yong-Ik

    1997-12-01

    We use B band CCD images to investigate the surface brightness distributions and dynamical properties of 29 Galactic globular clusters. Model fits suggest that 22 clusters show King type surface brightness profiles, while 7 clusters are characterized by power law cusp profiles. For the King type clusters, concentration parameters (c = log(rt =rc)) range from 1.20 to 2.10, and core radii are 0.4 to 1.9 pc. The mean value of power law slopes of 7 cuspy clusters was estimated as ¥á = 1.011 +/- 0.065. Total masses of King type globular clusters are in the range of 1.7 x 104M to 1.0 x 106M with a mean of 1.7 x 105M . A significant positive correlation between mass and mass-to-light ratio of King type globular clusters has been confirmed with a Pearson's correlation coefficient r = 0.52 and a confidence level of 99%. Our data also confirm a linear relation between total mass and absolute magnitude of King type globular clusters.

  19. Trazando la materia oscura con cúmulos globulares

    NASA Astrophysics Data System (ADS)

    Forte, J. C.

    Se describe la estrategia adoptada para mapear la distribución de materia oscura y bariónica en galaxias elípticas cuyos cúmulos globulares están siendo observados con los telescopios VLT y Gemini. Se ejemplifican los resultados con los datos obtenidos en el cúmulo de Fornax.

  20. Possible systematic decreases in the age of globular clusters

    SciTech Connect

    Shi, X.; Schramm, D. N.; Dearborn, D. S.P.; Truran, J. W.

    1994-03-01

    The ages of globular clusters inferred from observations depends sensitively on assumptions like the initial helium abundance and the mass loss rate. A high helium abundance (e.g., Y\\approx0.28) or a mass loss rate of \\sim10^{-11}M_\\odot yr^{-1} near the main sequence turn-off region lowers the current age estimate from 14 Gyr to about 10--12 Gyr, significantly relaxing the constraints on the Hubble constant, allowing values as high as 60km/sec/Mpc for a universe with the critical density and 90km/sec/Mpc for a baryon-only universe. Possible mechanisms for the helium enhancement in globular clusters are discussed, as are arguments for an instability strip induced mass loss near the turn-off. Ages lower than 10 Gyr are not possible even with the operation of both of these mechanisms unless the initial helium abundance in globular clusters is >0.30, which would conflict with indirect measurements of helium abundances in globular clusters.

  1. BVRI CCD photometry of the globular cluster NGC 2808

    SciTech Connect

    Alcaino, G.; Liller, W.; Alvarado, F.; Wenderoth, E. )

    1990-03-01

    As a part of a continuing program, CCD color-magnitude diagrams are presented for the bright globular cluster NGC 2808 in the four colors comprising BVRI. From a comparison of four different CMDs with theoretical isochrones, an age of 16 + or - 2 Gyr is obtained, assuming a value for Fe/H near -1.3. 28 refs.

  2. The Extended Globular Cluster System of NGC3923

    NASA Astrophysics Data System (ADS)

    Ahumada, Tomás; Miller, Bryan; Candlish, Graeme; McGaugh, Stacy S.; Mihos, Chris; Smith, Rory; Puzia, Thomas H.; Taylor, Matthew

    2017-01-01

    In the LambdaCMD paradigm of galaxy formation galaxy halos and their globular clusters systems build up over time by the accretion of small satellites. We can learn about this process in detail by observing systems with ongoing accretion events and comparing the data with simulations. Elliptical shell galaxies are systems that are thought to be due to ongoing or recent minor mergers. We present preliminary results of an investigation of the entire globular cluster system of the shell galaxy NGC3923 from deep DECam g and i-band imaging. Cluster candidates are selected using Principal Component Analysis of Sextractor/PSFEx parameters. We will present the 2D and radial distributions of the globular cluster candidates out to a projected radius of about 130kpc, or 26Re, making this one of the most extended cluster systems studied. We find that the bluer globular</