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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. Self-Assembly of Globular Protein-Polymer Diblock Copolymers

    NASA Astrophysics Data System (ADS)

    Thomas, C. S.; Olsen, B. D.

    2011-03-01

    The self-assembly of globular protein-polymer diblock copolymers into nanostructured phases is demonstrated as an elegant and simple method for structural control in biocatalysis or bioelectronics. In order to fundamentally investigate self-assembly in these complex block copolymer systems, a red fluorescent protein was expressed in E. coli and site-specifically conjugated to a low polydispersity poly(N-isopropyl acrylamide) (PNIPAM) block using thiol-maleimide coupling to form a well-defined model globular protein-polymer diblock. Functional protein materials are obtained by solvent evaporation and solvent annealing above and below the lower critical solution temperature of PNIPAM in order to access different pathways toward self-assembly. Small angle x-ray scattering and microscopy are used to show that the diblock forms lamellar nanostructures and to explore dependence of nanostructure formation on processing conditions. Circular dichroism and UV-vis show that a large fraction of the protein remains in its folded state after conjugation, and wide angle x-ray scattering demonstrates that diblock copolymer self-assembly changes the protein packing symmetry.

  9. 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

  10. 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.

  11. Scaling Rules for Vibrational Energy Transport in Globular Proteins.

    PubMed

    Buchenberg, Sebastian; Leitner, David M; Stock, Gerhard

    2016-01-07

    Computational studies of vibrational energy flow in biomolecules have to date mapped out transport pathways on a case-by-case basis. To provide a more general approach, we derive scaling rules for vibrational energy transport in a globular protein, which are identified from extensive nonequilibrium molecular dynamics simulations of vibrational energy flow in the villin headpiece subdomain HP36. We parametrize a master equation based on inter-residue, residue-solvent, and heater-residue energy-transfer rates, which closely reproduces the results of the all-atom simulations. From that fit, two scaling rules emerge, one for energy transport along the protein backbone which relies on a diffusion model and another for energy transport between tertiary contacts, which is based on a harmonic model. Requiring only the calculation of mean and variance of relatively few atomic distances, the approach holds the potential to predict the pathways and time scales of vibrational energy flow in large proteins.

  12. Nanomechanical properties of globular proteins: lactate oxidase.

    PubMed

    Parra, Ana; Casero, Elena; Lorenzo, Encarnación; Pariente, Félix; Vázquez, Luis

    2007-02-27

    We report on the study of the nanomechanical properties of a lactate oxidase (LOx) monolayer immobilized on gold substrates by atomic force microscopy techniques operating under buffer conditions. Topographical contact mode imaging evidenced the protein deformation under the applied tip load. We performed approaching force curves with both stiff and soft cantilevers by imposing maximum loads of 1.6 nN and 400 pN, respectively. We found that the experimental data were well fitted by the Hertz model for a conical indenter. The use of two types of cantilevers allowed us to check further the consistency of the applicability of the Hertz model to the experimental data. After analyzing 180 curves, we obtained an average value of Young's modulus for the LOx layer in the 0.5-0.8 GPa range. These results agreed with those obtained for LOx submonolayer deposits on mica substrates, which allows discarding any important contribution from the underlying substrate on the measured properties. This range of values is closer to those obtained by other techniques on other globular proteins in comparison with those reported in previous AFM studies on similar systems. We found that for our experimental conditions the force curves can be, in principle, well fitted by the Hertz model for both conical and spherical indenter geometries. However, as the Young's modulus obtained for both geometries can differ appreciably, it becomes necessary to assess which indenter geometry is more adequate to explain the experimental data. For such purpose a systematic study of the indentation versus applied force curves obtained from both fittings for all the experimental curves was done.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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).

  18. The nature of protein interactions governing globular protein-polymer block copolymer self-assembly.

    PubMed

    Lam, Christopher N; Kim, Minkyu; Thomas, Carla S; Chang, Dongsook; Sanoja, Gabriel E; Okwara, Chimdimma U; Olsen, Bradley D

    2014-04-14

    The effects of protein surface potential on the self-assembly of protein-polymer block copolymers are investigated in globular proteins with controlled shape through two approaches: comparison of self-assembly of mCherry-poly(N-isopropylacrylamide) (PNIPAM) bioconjugates with structurally homologous enhanced green fluorescent protein (EGFP)-PNIPAM bioconjugates, and mutants of mCherry with altered electrostatic patchiness. Despite large changes in amino acid sequence, the temperature-concentration phase diagrams of EGFP-PNIPAM and mCherry-PNIPAM conjugates have similar phase transition concentrations. Both materials form identical phases at two different coil fractions below the PNIPAM thermal transition temperature and in the bulk. However, at temperatures above the thermoresponsive transition, mCherry conjugates form hexagonal phases at high concentrations while EGFP conjugates form a disordered micellar phase. At lower concentration, mCherry shows a two-phase region while EGFP forms homogeneous disordered micellar structures, reflecting the effect of changes in micellar stability. Conjugates of four mCherry variants with changes to their electrostatic surface patchiness also showed minimal change in phase behavior, suggesting that surface patchiness has only a small effect on the self-assembly process. Measurements of protein/polymer miscibility, second virial coefficients, and zeta potential show that these coarse-grained interactions are similar between mCherry and EGFP, indicating that coarse-grained interactions largely capture the relevant physics for soluble, monomeric globular protein-polymer conjugate self-assembly.

  19. 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.

  20. Engineering Globular Protein Vesicles through Tunable Self-Assembly of Recombinant Fusion Proteins.

    PubMed

    Jang, Yeongseon; Choi, Won Tae; Heller, William T; Ke, Zunlong; Wright, Elizabeth R; Champion, Julie A

    2017-07-27

    Vesicles assembled from folded, globular proteins have potential for functions different from traditional lipid or polymeric vesicles. However, they also present challenges in understanding the assembly process and controlling vesicle properties. From detailed investigation of the assembly behavior of recombinant fusion proteins, this work reports a simple strategy to engineer protein vesicles containing functional, globular domains. This is achieved through tunable self-assembly of recombinant globular fusion proteins containing leucine zippers and elastin-like polypeptides. The fusion proteins form complexes in solution via high affinity binding of the zippers, and transition through dynamic coacervates to stable hollow vesicles upon warming. The thermal driving force, which can be tuned by protein concentration or temperature, controls both vesicle size and whether vesicles are single or bi-layered. These results provide critical information to engineer globular protein vesicles via self-assembly with desired size and membrane structure. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Universal features of fluctuations in globular proteins.

    PubMed

    Erman, Burak

    2016-06-01

    Using data from 2000 non-homologous protein crystal structures, we show that the distribution of residue B factors of proteins collapses onto a single master curve. We show by maximum entropy arguments that this curve is a Gamma function whose order and dispersion are obtained from experimental data. The distribution for any given specific protein can be generated from the master curve by a linear transformation. Any perturbation of the B factor distribution of a protein, imposed at constant energy, causes a decrease in the entropy of the protein relative to that of the reference state. Proteins 2016; 84:721-725. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Comparison of solid particles, globular proteins and surfactants as emulsifiers.

    PubMed

    Tcholakova, S; Denkov, N D; Lips, A

    2008-03-28

    The aim of this paper is to present a short overview of the main mechanisms operative in the formation and stabilization of emulsions by solid particles and, on this basis, to make comparisons between solid particles, surfactants and globular proteins as emulsifiers. When available, simple quantitative relations are presented, with the respective numerical estimates and discussion of the applicability of these relations to particle-stabilized systems. Non-obvious similarities between the different types of emulsifiers are outlined in several cases in which the description of the system can be performed at a phenomenological level. Examples are presented for the process of emulsification, where we show that several simple theoretical expressions, derived originally in the studies of surfactants and protein emulsifiers, can be successfully applied to particle-stabilized emulsions. In contrast, for the phenomena in which the detailed mechanisms of particle adsorption and film stabilization are important, the differences between the various emulsifiers prevail, thus making it impossible to use the same theoretical description. The most important specific characteristics of the solid particles which strongly affect their behavior are the high barrier to particle adsorption, high desorption energy and strong capillary forces between particles trapped in liquid films, which all originate in the relatively large particle size (as compared to the size of surfactant and protein molecules). The capillary mechanism of stabilization of liquid films by solid particles is reviewed in some detail, to emphasize its specific features and to demonstrate the applicability of several simple expressions for approximate estimates. Interestingly, we found that the hypothesis for some exceptionally high coalescence stability of the particle-stabilized emulsions is not supported by the experimental data available in literature. On the other hand, the particles are able to completely arrest

  3. 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

  4. Selective Uptake and Refolding of Globular Proteins in Coacervate Microdroplets.

    PubMed

    Martin, Nicolas; Li, Mei; Mann, Stephen

    2016-06-14

    Intrinsic differences in the molecular sequestration of folded and unfolded proteins within poly(diallyldimethylammonium) (PDDA)/poly(acrylate) (PAA) coacervate microdroplets are exploited to establish membrane-free microcompartments that support protein refolding, facilitate the recovery of secondary structure and enzyme activity, and enable the selective uptake and exclusion of folded and unfolded biomolecules, respectively. Native bovine serum albumin, carbonic anhydrase, and α-chymotrypsin are preferentially sequestered within positively charged coacervate microdroplets, and the unfolding of these proteins in the presence of increasing amounts of urea results in an exponential decrease in the equilibrium partition constants as well as the kinetic release of unfolded molecules from the droplets into the surrounding continuous phase. Slow refolding in the presence of positively charged microdroplets leads to the resequestration of functional proteins and the restoration of enzymatic activity; however, fast refolding results in protein aggregation at the droplet surface. In contrast, slow and fast refolding in the presence of negatively charged PDDA/PAA droplets gives rise to reduced protein aggregation and misfolding by interactions at the droplet surface to give increased levels of protein renaturation. Together, our observations provide new insights into the bottom-up design and construction of self-assembling microcompartments capable of supporting the selective uptake and refolding of globular proteins.

  5. 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.

  6. 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.

  7. 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.

  8. Strong Keratin-like Nanofibers Made of Globular Protein

    NASA Astrophysics Data System (ADS)

    Dror, Yael; Makarov, Vadim; Admon, Arie; Zussman, Eyal

    2008-03-01

    Protein fibers as elementary structural and functional elements in nature inspire the engineering of protein-based products for versatile bio-medical applications. We have recently used the electrospinning process to fabricate strong sub-micron fibers made solely of serum albumin (SA). This raises the challenges of turning a globular non-viscous protein solution into a polymer--like spinnable solution and producing keratin-like fibers enriched in inter S-S bridges. A stable spinning process was achieved by using SA solution in a rich trifluoroethanol-water mixture with β-mercaptoethanol. The breakage of the intra disulfide bridges, as identified by mass spectrometry, together with the denaturing alcohol, enabled a pronounced expansion of the protein. This in turn, affects the rheological properties of the solution. X-ray diffraction pattern of the fibers revealed equatorial orientation, indicating the alignment of structures along the fiber axis. The mechanical properties reached remarkable average values (Young's modulus of 1.6GPa, and max stress of 36MPa) as compared to other fibrous protein nanofibers. These significant results are attributed to both the alignment and inter disulfide bonds (cross linking) that were formed by spontaneous post-spinning oxidation.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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).

  1. Formation and stability of secondary structures in globular proteins

    NASA Astrophysics Data System (ADS)

    Bascle, J.; Garel, T.; Orland, H.

    1993-02-01

    We study two models for the formation and packing of helices and sheets in globular (compact) proteins. These models, based on weighted Hamiltonian paths on a regular lattice both exhibit a first order transition between a compact high temperature phase, with no extended secondary structures, and a quasi-frozen compact phase, with secondary structures invading the whole lattice. The quasi-frozen phase with very weak temperature dependence, is identified as the native phase of proteins, whereas the high-temperature phase may be relevant to the so-called molten globule state of proteins. Nous étudions deux modèles pour la formation et l'empilement d'hélices ou de feuillets dans la phase globulaire (compacte) des protéines. ces modèles, fondés sur des chemins hamiltoniens pondérés sur réseau, possèdent une transition de phase du premier ordre, entre (i) une phase haute température compacte, avec structures secondaires non étendues, et (ii) une phase compacte quasi-gelée, où les structures secondaires envahissent tout le réseau. La phase quasi-gelée, qui a une dépendance en température très faible, est identifiée à la phase native des protéines; la phase haute température est peut-être reliée à la phase native “globule fondu” (molten globule) des protéines.

  2. 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.

  3. 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.

  4. 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.

  5. A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope

    DOE PAGES

    Abdo, A. A.

    2010-11-24

    Context. Globular clusters with their large populations of millisecond pulsars (MSPs) are believed to be potential emitters of high-energy gamma-ray emission. The observation of this emission provides a powerful tool to assess the millisecond pulsar population of a cluster, is essential for understanding the importance of binary systems for the evolution of globular clusters, and provides complementary insights into magnetospheric emission processes. Aims. Our goal is to constrain the millisecond pulsar populations in globular clusters from analysis of gamma-ray observations. Methods. We use 546 days of continuous sky-survey observations obtained with the Large Area Telescope aboard the Fermi Gamma-ray Spacemore » Telescope to study the gamma-ray emission towards 13 globular clusters. Results. Steady point-like high-energy gamma-ray emission has been significantly detected towards 8 globular clusters. Five of them (47 Tucanae, Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices (0.7 < Γ < 1.4) and clear evidence for an exponential cut-off in the range 1.0 - 2.6 GeV, which is the characteristic signature of magnetospheric emission from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral indices (1.0 < Γ < 1.7), however the presence of an exponential cut-off can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC 6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral properties. From the observed gamma-ray luminosities, we estimate the total number of MSPs that is expected to be present in these globular clusters. We show that our estimates of the MSP population correlate with the stellar encounter rate and we estimate 2600 - 4700 MSPs in Galactic globular clusters, commensurate with previous estimates. Conclusions. The observation of high-energy gamma-ray emission from globular clusters thus provides a reliable independent method to assess their millisecond pulsar populations.« less

  6. Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability.

    PubMed

    Venturoli, Daniele; Rippe, Bengt

    2005-04-01

    Polydisperse mixtures of dextran or Ficoll have been frequently used as molecular probes for studies of glomerular permselectivity because they are largely inert and not processed (reabsorbed) by the proximal tubules. However, dextrans are linear, flexible molecules, which apparently are hyperpermeable across the glomerular barrier. By contrast, the Ficoll molecule is almost spherical. Still, there is ample evidence that Ficoll fractional clearances (sieving coefficients) across the glomerular capillary wall (GCW) are markedly higher than those for neutral globular proteins of an equivalent in vitro Stokes-Einstein (SE) radius. Physical data, obtained by "crowding" experiments or measurements of intrinsic viscosity, suggest that the Ficoll molecule exhibits a rather open, deformable structure and thus deviates from an ideally hard sphere. This is also indicated from the relationship between (log) in vitro SE radius and (log) molecular weight (MW). Whereas globular proteins seem to behave in a way similar to hydrated hard spheres, polydisperse dextran and Ficoll exhibit in vitro SE radii that are much larger than those for compact spherical molecules of equivalent MW. For dextran, this can be partially explained by a high-molecular-size asymmetry. However, for Ficoll the explanation may be that the Ficoll molecule is more flexible (deformable) than are globular proteins. An increased compressibility of Ficoll and an increased deformability and size asymmetry for dextran may be the explanation for the fact that the permeability of the GCW is significantly higher when assessed using polysaccharides such as Ficoll or dextran compared with that obtained using globular proteins as molecular size probes. We suggest that molecular deformability, besides molecular size, shape, and charge, plays a crucial role in determining the glomerular permeability to molecules of different species.

  7. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Salt-bridge networks within globular and disordered proteins: characterizing trends for designable interactions.

    PubMed

    Basu, Sankar; Mukharjee, Debasish

    2017-07-01

    There has been considerable debate about the contribution of salt bridges to the stabilization of protein folds, in spite of their participation in crucial protein functions. Salt bridges appear to contribute to the activity-stability trade-off within proteins by bringing high-entropy charged amino acids into close contacts during the course of their functions. The current study analyzes the modes of association of salt bridges (in terms of networks) within globular proteins and at protein-protein interfaces. While the most common and trivial type of salt bridge is the isolated salt bridge, bifurcated salt bridge appears to be a distinct salt-bridge motif having a special topology and geometry. Bifurcated salt bridges are found ubiquitously in proteins and interprotein complexes. Interesting and attractive examples presenting different modes of interaction are highlighted. Bifurcated salt bridges appear to function as molecular clips that are used to stitch together large surface contours at interacting protein interfaces. The present work also emphasizes the key role of salt-bridge-mediated interactions in the partial folding of proteins containing long stretches of disordered regions. Salt-bridge-mediated interactions seem to be pivotal to the promotion of "disorder-to-order" transitions in small disordered protein fragments and their stabilization upon binding. The results obtained in this work should help to guide efforts to elucidate the modus operandi of these partially disordered proteins, and to conceptualize how these proteins manage to maintain the required amount of disorder even in their bound forms. This work could also potentially facilitate explorations of geometrically specific designable salt bridges through the characterization of composite salt-bridge networks. Graphical abstract ᅟ.

  9. 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

  10. Dynamics of a globular protein adsorbed to liposomal nanoparticles.

    PubMed

    Ceccon, Alberto; Lelli, Moreno; D'Onofrio, Mariapina; Molinari, Henriette; Assfalg, Michael

    2014-09-24

    A solution-state NMR method is proposed to investigate the dynamics of proteins that undergo reversible association with nanoparticles (NPs). We applied the recently developed dark-state exchange saturation transfer experiment to obtain residue-level dynamic information on a NP-adsorbed protein in the form of transverse spin relaxation rates, R2bound. Based on dynamic light scattering, fluorescence, circular dichroism, and NMR spectroscopy data, we show that the test protein, human liver fatty acid binding protein, interacts reversibly and peripherally with liposomal NPs without experiencing significant structural changes. The significant but modest saturation transfer from the bound state observed at 14.1 and 23.5 T static magnetic fields, and the small determined R2bound values were consistent with a largely unrestricted global motion at the lipid surface. Amino acid residues displaying faster spin relaxation mapped to a region that could represent the epitope of interaction with an extended phospholipid chain constituting the protein anchor. These results prove that atomic-resolution protein dynamics is accessible even after association with NPs, supporting the use of saturation transfer methods as powerful tools in bionanoscience.

  11. 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.

  12. Solid-state nanostructured materials from self-assembly of a globular protein-polymer diblock copolymer.

    PubMed

    Thomas, Carla S; Glassman, Matthew J; Olsen, Bradley D

    2011-07-26

    Self-assembly of three-dimensional solid-state nanostructures containing approximately 33% by weight globular protein is demonstrated using a globular protein-polymer diblock copolymer, providing a route to direct nanopatterning of proteins for use in bioelectronic and biocatalytic materials. A mutant red fluorescent protein, mCherryS131C, was prepared by incorporation of a unique cysteine residue and site-specifically conjugated to end-functionalized poly(N-isopropylacrylamide) through thiol-maleimide coupling to form a well-defined model protein-polymer block copolymer. The block copolymer was self-assembled into bulk nanostructures by solvent evaporation from concentrated solutions. Small-angle X-ray scattering and transmission electron microscopy illustrated the formation of highly disordered lamellae or hexagonally perforated lamellae depending upon the selectivity of the solvent during evaporation. Solvent annealing of bulk samples resulted in a transition toward lamellar nanostructures with mCherry packed in a bilayer configuration and a large improvement in long-range ordering. Wide-angle X-ray scattering indicated that mCherry did not crystallize within the block copolymer nanodomains and that the β-sheet spacing was not affected by self-assembly. Circular dichroism showed no change in protein secondary structure after self-assembly, while UV-vis spectroscopy indicated approximately 35% of the chromophore remained optically active.

  13. Solid-State Nanostructured Materials from Self-Assembly of a Globular Protein-Polymer Diblock Copolymer

    PubMed Central

    Thomas, Carla S.; Glassman, Matthew J.; Olsen, Bradley D.

    2014-01-01

    Self-assembly of three-dimensional solid-state nanostructures containing approximately 33% by weight globular protein is demonstrated using a globular protein-polymer diblock copolymer, providing a route to direct nanopatterning of proteins for use in bioelectronic and biocatalytic materials. A mutant red fluorescent protein, mCherryS131C, was prepared by incorporation of a unique cysteine residue and site-specifically conjugated to end-functionalized poly(N-isopropylacrylamide) through thiol-maleimide coupling to form a well-defined model protein-polymer block copolymer. The block copolymer was self-assembled into bulk nanostructures by solvent evaporation from concentrated solutions. Small-angle X-ray scattering and transmission electron microscopy illustrated the formation of highly disordered lamellae or hexagonally perforated lamellae depending upon the selectivity of the solvent during evaporation. Solvent annealing of bulk samples resulted in a transition towards lamellar nanostructures with mCherry packed in a bilayer configuration and a large improvement in long range ordering. Wide-angle X-ray scattering indicated that mCherry did not crystallize within the block copolymer nanodomains and that the β-sheet spacing was not affected by self-assembly. Circular dichroism showed no change in protein secondary structure after self-assembly, while UV-vis spectroscopy indicated approximately 35% of the chromophore remained optically active. PMID:21696135

  14. [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.

  15. 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.

  16. 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.

  17. 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

  18. 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).

  19. 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

  20. 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.

  1. 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.

  2. Nucleic acid induced unfolding of recombinant prion protein globular fragment is pH dependent.

    PubMed

    Bera, Alakesh; Nandi, Pradip K

    2014-12-01

    Nucleic acid can catalyze the conversion of α-helical cellular prion protein to β-sheet rich Proteinase K resistant prion protein oligomers and amyloid polymers in vitro and in solution. Because unfolding of a protein molecule from its ordered α-helical structure is considered to be a necessary step for the structural conversion to its β-sheet rich isoform, we have studied the unfolding of the α-helical globular 121-231 fragment of mouse recombinant prion protein in the presence of different nucleic acids at neutral and acid pH. Nucleic acids, either single or double stranded, do not have any significant effect on the secondary structure of the protein fragment at neutral pH; however the protein secondary structure is modified by the nucleic acids at pH 5. Nucleic acids do not show any significant effect on the temperature induced unfolding of the globular prion protein domain at neutral pH which, however, undergoes a gross conformational change at pH 5 as evidenced from the lowering of the midpoint of thermal denaturation temperatures, Tm, of the protein. The extent of Tm decrease shows a dependence on the nature of nucleic acid. The interaction of nucleic acid with the nonpolar groups exposed from the protein interior at pH 5 probably contributes substantially to the unfolding process of the protein. © 2014 The Protein Society.

  3. 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

    2017-05-01

    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 that form during hydrostatic burning in massive stars. NGC 1718 is also enhanced in La, suggesting that it was enriched in ejecta from metal-poor asymptotic giant branch stars.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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).

  9. Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells.

    PubMed Central

    Arrio-Dupont, M; Foucault, G; Vacher, M; Devaux, P F; Cribier, S

    2000-01-01

    Modulated fringe pattern photobleaching (MFPP) was used to measure the translational diffusion of microinjected fluorescein isothiocyanate (FITC)-labeled proteins of different sizes in the cytoplasm of cultured muscle cells. This technique, which is an extension of the classical fluorescence recovery after photobleaching (FRAP) technique, allows the measurement of the translational diffusion of macromolecules over several microns. Proteins used had molecular masses between 21 and 540 kDa. The results clearly indicated that the diffusivity of the various proteins is a decreasing function of their hydrodynamic radius. This decrease is more rapid with globular proteins than with FITC-labeled dextrans (, Biophys. J. 70:2327-2332), most likely because, unlike globular proteins, dextrans are randomly coiled macromolecules with a flexible structure. These data do not exclude the possibility of a rapid diffusion over a short distance, unobservable with our experimental set-up, which would take place within the first milliseconds after bleaching and would correspond to the diffusion in restricted domains followed by impeded diffusion provoked by the network of microtubules, microfilaments, and intermediate filaments. Thus our results may complement rather than contradict those of Verkman and collaborators (, J. Cell Biol. 138:1-12). The biological consequence of the size-dependent restriction of the mobility of proteins in the cell cytoplasm is that the formation of intracellular complexes with other proteins considerably reduces their mobility. PMID:10653802

  10. Solution Self-Assembly of Globular Protein-Polymer Conjugate Block Copolymers

    NASA Astrophysics Data System (ADS)

    Olsen, Bradley

    2014-03-01

    Controlling the nanostructured self-assembly of globular proteins and enzymes can significantly advance the applications of soft materials as catalysts, sensors, and medical materials. However, the incorporation of globular proteins as one block in the block copolymer introduces changes in chain shape, chain entropy, and specific interactions that significantly impact the thermodynamics of self-assembly. Here, we explore the self-assembly of model globular protein-polymer block copolymers in concentrated solutions to form nanostructured materials. A phase diagram as a function of concentration and temperature for a model material mCherry-poly(N-isopropylacrylamide) (PNIPAM) is asymmetric, showing hexagonal cylinders for coil fractions less than 0.5 and a lamellar ordering for coil fractions greater than 0.5, divided by a narrow region of hexagonally perforated lamellae. Order-order transitions as a function of temperature are driven by the thermoresponsive desolvation of PNIPAM. Surprisingly, the materials exhibit reentrant order-disorder transition behavior, such that the conjugate block copolymers are disordered at both low and high concentrations but well-ordered at intermediate concentrations. Changing the polymer chemistry to monomers with different types of hydrogen bonding results in significant changes in the self-assembly, including the observation of a cubic phase that shows the same scattering pattern as the gyroid phase observed in traditional block copolymers. The choice of polymer also has a strong impact on the order-disorder transition concentration, demonstrating that the polymer-protein interaction plays a significant role in governing self-assembly in solution. Consistent with this effect, the order-disorder transition concentration is minimized in symmetric conjugates. Changing the protein from mCherry to myoglobin results in a reduction in ordering, suggesting that the regularity of the protein shape is important. This research was supported by

  11. 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

  12. 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.

  13. 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.

  14. A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope

    SciTech Connect

    Abdo, A. A.

    2010-11-24

    Context. Globular clusters with their large populations of millisecond pulsars (MSPs) are believed to be potential emitters of high-energy gamma-ray emission. The observation of this emission provides a powerful tool to assess the millisecond pulsar population of a cluster, is essential for understanding the importance of binary systems for the evolution of globular clusters, and provides complementary insights into magnetospheric emission processes. Aims. Our goal is to constrain the millisecond pulsar populations in globular clusters from analysis of gamma-ray observations. Methods. We use 546 days of continuous sky-survey observations obtained with the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope to study the gamma-ray emission towards 13 globular clusters. Results. Steady point-like high-energy gamma-ray emission has been significantly detected towards 8 globular clusters. Five of them (47 Tucanae, Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices (0.7 < Γ < 1.4) and clear evidence for an exponential cut-off in the range 1.0 - 2.6 GeV, which is the characteristic signature of magnetospheric emission from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral indices (1.0 < Γ < 1.7), however the presence of an exponential cut-off can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC 6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral properties. From the observed gamma-ray luminosities, we estimate the total number of MSPs that is expected to be present in these globular clusters. We show that our estimates of the MSP population correlate with the stellar encounter rate and we estimate 2600 - 4700 MSPs in Galactic globular clusters, commensurate with previous estimates. Conclusions. The observation of high-energy gamma-ray emission from globular clusters thus provides a reliable independent method to assess their millisecond pulsar populations.

  15. 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

  16. 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.

  17. Creep anomaly in electrospun fibers made of globular proteins

    NASA Astrophysics Data System (ADS)

    Regev, Omri; Arinstein, Arkadii; Zussman, Eyal

    2013-12-01

    The anomalous responses of electrospun nanofibers and film fabricated of unfolded bovine serum albumin (BSA) under constant stress (creep) is observed. In contrast to typical creep behavior of viscoelastic materials demonstrating (after immediate elastic response) a time-dependent elongation, in case of low applied stresses (<1 MPa) the immediate elastic response of BSA samples is followed by gradual contraction up to 2%. Under higher stresses (2-6 MPa) the contraction phase changes into elongation; and in case of stresses above 7 MPa only elongation was observed, with no initial contraction. The anomalous creep behavior was not observed when the BSA samples were subjected to additional creep cycles independently on the stress level. The above anomaly, which was not observed before either for viscoelastic solids or for polymers, is related to specific protein features, namely, to the ability to fold. We hypothesize that the phenomenon is caused by folding of BSA macromolecules into dry molten globule states, feasible after cross-linked bonds break up, resulting from the applied external force.

  18. 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.

  19. 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.

  20. 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.

    2017-04-01

    We present a photometric study of the prototype merger remnant NGC 3610 and its globular cluster (GC) system, based on new Gemini/GMOS and Advanced Camera for Surveys/Hubble Space Telescope archival images. Thanks to the large field of view of our GMOS data, larger than previous studies, we are able to detect a 'classical' bimodal GC colour distribution, corresponding to 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 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Kinetically Controlled Nanostructure Formation in Self-Assembled Globular Protein-Polymer Diblock Copolymers

    PubMed Central

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

    2014-01-01

    Aqueous processing of globular protein-polymer diblock copolymers into solid-state materials and subsequent solvent annealing enables kinetic and thermodynamic control of nanostructure formation to produce block copolymer morphologies that maintain a high degree of protein fold and function. Using model diblock copolymers composed of mCherry-b-poly(N-isopropylacrylamide), orthogonal control over solubility of the protein block through changes in pH and the polymer block through changes in temperature is demonstrated during casting and solvent annealing. Hexagonal cylinders, perforated lamellae, lamellae, or hexagonal and disordered micellar phases are observed depending upon the coil fraction of the block copolymer and the kinetic pathway used for self-assembly. Good solvents for the polymer block produce ordered structures reminiscent of coil-coil diblock copolymers, while an unfavorable solvent results in kinetically trapped micellar structures. Decreasing solvent quality for the protein improves long-range ordering, suggesting that the strength of protein interactions influences nanostructure formation. Subsequent solvent annealing results in evolution of the nanostructures, with the best ordering and the highest protein function observed when annealing in a good solvent for both blocks. While protein secondary structure was found to be almost entirely preserved for all processing pathways, UV-vis spectroscopy of solid-state films indicates that using a good solvent for the protein block enables up to 70% of the protein to be retained in its functional form. PMID:22924842

  6. Kinetically controlled nanostructure formation in self-assembled globular protein-polymer diblock copolymers.

    PubMed

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

    2012-09-10

    Aqueous processing of globular protein-polymer diblock copolymers into solid-state materials and subsequent solvent annealing enables kinetic and thermodynamic control of nanostructure formation to produce block copolymer morphologies that maintain a high degree of protein fold and function. When model diblock copolymers composed of mCherry-b-poly(N-isopropylacrylamide) are used, orthogonal control over solubility of the protein block through changes in pH and the polymer block through changes in temperature is demonstrated during casting and solvent annealing. Hexagonal cylinders, perforated lamellae, lamellae, or hexagonal and disordered micellar phases are observed, depending on the coil fraction of the block copolymer and the kinetic pathway used for self-assembly. Good solvents for the polymer block produce ordered structures reminiscent of coil-coil diblock copolymers, while an unfavorable solvent results in kinetically trapped micellar structures. Decreasing solvent quality for the protein improves long-range ordering, suggesting that the strength of protein interactions influences nanostructure formation. Subsequent solvent annealing results in evolution of the nanostructures, with the best ordering and the highest protein function observed when annealing in a good solvent for both blocks. While protein secondary structure was found to be almost entirely preserved for all processing pathways, UV-vis spectroscopy of solid-state films indicates that using a good solvent for the protein block enables up to 70% of the protein to be retained in its functional form.

  7. Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

    PubMed

    Pang, Yuan-Ping

    2016-09-01

    Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å(2) for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å(2) for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

  8. 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.

  9. [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.

  10. A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins.

    PubMed

    Tsolis, Antonios C; Papandreou, Nikos C; Iconomidou, Vassiliki A; Hamodrakas, Stavros J

    2013-01-01

    The purpose of this work was to construct a consensus prediction algorithm of 'aggregation-prone' peptides in globular proteins, combining existing tools. This allows comparison of the different algorithms and the production of more objective and accurate results. Eleven (11) individual methods are combined and produce AMYLPRED2, a publicly, freely available web tool to academic users (http://biophysics.biol.uoa.gr/AMYLPRED2), for the consensus prediction of amyloidogenic determinants/'aggregation-prone' peptides in proteins, from sequence alone. The performance of AMYLPRED2 indicates that it functions better than individual aggregation-prediction algorithms, as perhaps expected. AMYLPRED2 is a useful tool for identifying amyloid-forming regions in proteins that are associated with several conformational diseases, called amyloidoses, such as Altzheimer's, Parkinson's, prion diseases and type II diabetes. It may also be useful for understanding the properties of protein folding and misfolding and for helping to the control of protein aggregation/solubility in biotechnology (recombinant proteins forming bacterial inclusion bodies) and biotherapeutics (monoclonal antibodies and biopharmaceutical proteins).

  11. Globularity-Selected Large Molecules for a New Generation of Multication Perovskites.

    PubMed

    Gholipour, Somayeh; Ali, Abdollah Morteza; Correa-Baena, Juan-Pablo; Turren-Cruz, Silver-Hamill; Tajabadi, Fariba; Tress, Wolfgang; Taghavinia, Nima; Grätzel, Michael; Abate, Antonio; De Angelis, Filippo; Gaggioli, Carlo Alberto; Mosconi, Edoardo; Hagfeldt, Anders; Saliba, Michael

    2017-08-18

    Perovskite solar cells (PSCs) use perovskites with an APbX3 structure, where A is a monovalent cation and X is a halide such as Cl, Br, and/or I. Currently, the cations for high-efficiency PSCs are Rb, Cs, methylammonium (MA), and/or formamidinium (FA). Molecules larger than FA, such as ethylammonium (EA), guanidinium (GA), and imidazolium (IA), are usually incompatible with photoactive "black"-phase perovskites. Here, novel molecular descriptors for larger molecular cations are introduced using a "globularity factor", i.e., the discrepancy of the molecular shape and an ideal sphere. These cationic radii differ significantly from previous reports, showing that especially ethylammonium (EA) is only slightly larger than FA. This makes EA a suitable candidate for multication 3D perovskites that have potential for unexpected and beneficial properties (suppressing halide segregation, stability). This approach is tested experimentally showing that surprisingly large quantities of EA get incorporated, in contrast to most previous reports where only small quantities of larger molecular cations can be tolerated as "additives". MA/EA perovskites are characterized experimentally with a band gap ranging from 1.59 to 2.78 eV, demonstrating some of the most blue-shifted PSCs reported to date. Furthermore, one of the compositions, MA0.5 EA0.5 PbBr3 , shows an open circuit voltage of 1.58 V, which is the highest to date with a conventional PSC architecture. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Mutational analysis of the propensity for amyloid formation by a globular protein

    PubMed Central

    Chiti, Fabrizio; Taddei, Niccolò; Bucciantini, Monica; White, Paul; Ramponi, Giampietro; Dobson, Christopher M.

    2000-01-01

    Acylphosphatase can be converted in vitro, by addition of trifluoroethanol (TFE), into amyloid fibrils of the type observed in a range of human diseases. The propensity to form fibrils has been investigated for a series of mutants of acylphosphatase by monitoring the range of TFE concentrations that result in aggregation. We have found that the tendency to aggregate correlates inversely with the conformational stability of the native state of the protein in the different mutants. In accord with this, the most strongly destabilized acylphosphatase variant forms amyloid fibrils in aqueous solution in the absence of TFE. These results show that the aggregation process that leads to amyloid deposition takes place from an ensemble of denatured conformations under conditions in which non-covalent interactions are still favoured. These results support the hypothesis that the stability of the native state of globular proteins is a major factor preventing the in vivo conversion of natural proteins into amyloid fibrils under non-pathological conditions. They also suggest that stabilizing the native states of amyloidogenic proteins could aid prevention of amyloidotic diseases. PMID:10747012

  1. A real valued Genetic Algorithm for generating native like structure of small globular protein.

    PubMed

    Madhusmita, S; Singh, Harjinder; Karlapalem, Kamalakar; Mitra, Abhijit

    2008-01-01

    Predicting the 3D native conformation of a protein given the amino acid sequence is known as protein structure prediction (PSP) problem and is one of the greatest challenges of computational biology. The current work uses a real valued Genetic Algorithm (GA), a powerful variate of GA to simulate the PSP problem. This algorithm consists of basic evolutionary operators and a fitness vector. The fitness vector is designed by combining a set of knowledge based biophysical filters viz. persistence length, radius of gyration, packing fraction, hydrophobicity ratio and irregularity index of phi and psi. This vector converts all these biophysical measures into a real value by using specific weights or factors. The algorithm has been validated on six known globular proteins, with their length varying from 17-61 residues and total number of helices and strands in the range of 2-4. For all the test protein the algorithm converges rapidly and the converged structure shows a backbone RMSD (root mean square deviation) of 3-6A as compared to the native structure.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. Modification of structure and pattern of lipid monolayer on water and solid surfaces in presence of globular protein

    NASA Astrophysics Data System (ADS)

    Sah, Bijay Kumar; Kundu, Sarathi

    2017-05-01

    Langmuir monolayers of phospholipids at the air-water interface are well-established model systems for mimicking biological membranes and hence are useful for studying lipid-protein interactions. In the present work, phases and phase transformations occurring in the lipid (DMPA) monolayer in the presence of globular protein (BSA) at neutral subphase pH (≈7.0) are highlighted and the corresponding in-plane pattern and morphology are explored from the surface pressure (π) - specific molecular area (A) isotherm, Brewster angle microscopy (BAM) and atomic force microscopy (AFM) both at air-water and air-solid interfaces. Films of pure lipid and lipid-protein complexes are deposited on solid surfaces by Langmuir-Blodgett method. Due to the presence of BSA molecules, phases and domain pattern changes in comparison with that of the pure DMPA. Moreover, accumulations of globular proteins in between lipid domains are also visible through BAM. AFM shows that the mixed film has relatively bigger globular-like morphology in comparison with that of pure DMPA domains. Combination of electrostatic and hydrophobic interactions between protein and lipid are responsible for such modifications.

  7. 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

  8. Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes.

    PubMed

    Sivakamasundari, Chandrasekaran; Nagaraj, Ramakrishnan

    2009-06-01

    We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from -1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide-membrane interactions.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Structure, dynamics, and energetics of water at the surface of a small globular protein: A molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Dastidar, Shubhra Ghosh; Mukhopadhyay, Chaitali

    2003-08-01

    The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 °C lower than the average temperature of the system (27 °C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 Å from the protein surface.

  17. 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.

  18. 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).

  19. Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels.

    PubMed

    Miroux, B; Walker, J E

    1996-07-19

    We have investigated the over-production of seven membrane proteins in an Escherichia coli-bacteriophage T7 RNA polymerase expression system. In all seven cases, when expression of the target membrane protein was induced, most of the BL21(DE3) host cells died. Similar effects were also observed with expression vectors for ten globular proteins. Therefore, protein over-production in this expression system is either limited or prevented by bacterial cell death. From the few survivors of BL21(DE3) expressing the oxoglutarate-malate carrier protein from mitochondrial membranes, a mutant host C41(DE3) was selected that grew to high saturation cell density, and produced the protein as inclusion bodies at an elevated level without toxic effect. Some proteins that were expressed poorly in BL21(DE3), and others where the toxicity of the expression plasmids prevented transformation into this host, were also over-produced successfully in C41(DE3). The examples include globular proteins as well as membrane proteins, and therefore, strain C41(DE3) is generally superior to BL21(DE3) as a host for protein over-expression. However, the toxicity of over-expression of some of the membrane proteins persisted partially in strain C41(DE3). Therefore, a double mutant host C43(DE3) was selected from C41(DE3) cells containing the expression plasmid for subunit b of bacterial F-ATPase. In strain C43(DE3), both subunits b and c of the F-ATPase, an alanine-H(+) symporter, and the ADP/ATP and the phosphate carriers from mitochondria were all over-produced. The transcription of the gene for the OGCP and subunit b was lower in C41(DE3) and C43(DE3), respectively, than in BL21(DE3). In C43(DE3), the onset of transcription of the gene for subunit b was delayed after induction, and the over-produced protein was incorporated into the membrane. The procedure used for selection of C41(DE3) and C43(DE3) could be employed to tailor expression hosts in order to overcome other toxic effects associated

  20. 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.

  1. Formaldehyde at Low Concentration Induces Protein Tau into Globular Amyloid-Like Aggregates In Vitro and In Vivo

    PubMed Central

    Nie, Chun Lai; Wei, Yan; Chen, Xinyong; Liu, Yan Ying; Dui, Wen; Liu, Ying; Davies, Martyn C.; Tendler, Saul J.B.; He, Rong Giao

    2007-01-01

    Recent studies have shown that neurodegeneration is closely related to misfolding and aggregation of neuronal tau. Our previous results show that neuronal tau aggregates in formaldehyde solution and that aggregated tau induces apoptosis of SH-SY5Y and hippocampal cells. In the present study, based on atomic force microscopy (AFM) observation, we have found that formaldehyde at low concentrations induces tau polymerization whilst acetaldehyde does not. Neuronal tau misfolds and aggregates into globular-like polymers in 0.01–0.1% formaldehyde solutions. Apart from globular-like aggregation, no fibril-like polymerization was observed when the protein was incubated with formaldehyde for 15 days. SDS-PAGE results also exhibit tau polymerizing in the presence of formaldehyde. Under the same experimental conditions, polymerization of bovine serum albumin (BSA) or α-synuclein was not markedly detected. Kinetic study shows that tau significantly misfolds and polymerizes in 60 minutes in 0.1% formaldehyde solution. However, presence of 10% methanol prevents protein tau from polymerization. This suggests that formaldehyde polymerization is involved in tau aggregation. Such aggregation process is probably linked to the tau's special “worm-like” structure, which leaves the ε-amino groups of Lys and thiol groups of Cys exposed to the exterior. Such a structure can easily bond to formaldehyde molecules in vitro and in vivo. Polymerizing of formaldehyde itself results in aggregation of protein tau. Immunocytochemistry and thioflavin S staining of both endogenous and exogenous tau in the presence of formaldehyde at low concentrations in the cell culture have shown that formaldehyde can induce tau into amyloid-like aggregates in vivo during apoptosis. The significant protein tau aggregation induced by formaldehyde and the severe toxicity of the aggregated tau to neural cells may suggest that toxicity of methanol and formaldehyde ingestion is related to tau misfolding and

  2. Structural features that predict real-value fluctuations of globular proteins.

    PubMed

    Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

    2012-05-01

    It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. Copyright © 2012 Wiley Periodicals, Inc.

  3. 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

  4. On relationships between surfactant type and globular proteins interactions in solution.

    PubMed

    Blanco, Elena; Ruso, Juan M; Prieto, Gerardo; Sarmiento, Félix

    2007-12-01

    The binding of sodium perfluorooctanoate (C8FONa), sodium octanoate (C8HONa), lithium perfluorooctanoate (C8FOLi), and sodium dodecanoate (C12HONa) onto myoglobin, ovalbumin, and catalase in water has been characterized using electrophoretic mobility. The tendency of the protein-surfactant complexes to change their charge in the order catalase < ovalbumin < myoglobin was observed which was related to the contents of alpha-helices in the proteins. alpha-Helices are more hydrophobic than beta-sheets. The effect of surfactant on the zeta potentials follows C8HONa < C8FONa < C8FOLi < C12HONa for catalase and ovalbumin; and C8HONa < C8FOLi < C8FONa < C12HONa for myoglobin. The numbers of binding sites on the proteins were determined from the observed increases of the zeta-potential as a function of surfactant concentration in the regions where the binding was a consequence of the hydrophobic effect. The Gibbs energies of binding of the surfactants onto the proteins were evaluated. For all systems, Gibbs energies are negative and large at low concentrations (where binding to the high energy sites takes place) and become less negative at higher ones. This fact suggests a saturation process. Changes in Gibbs energies with the different proteins and surfactants under study have been found to follow same sequence than that found for the charge. The role of hydrophobic interactions in these systems has been demonstrated to be the predominant.

  5. Short amino acid stretches can mediate amyloid formation in globular proteins: The Src homology 3 (SH3) case

    PubMed Central

    Ventura, Salvador; Zurdo, Jesús; Narayanan, Saravanakumar; Parreño, Matilde; Mangues, Ramón; Reif, Bernd; Chiti, Fabrizio; Giannoni, Elisa; Dobson, Christopher M.; Aviles, Francesc X.; Serrano, Luis

    2004-01-01

    Protein misfolding and deposition underlie an increasing number of debilitating human disorders. We have shown that model proteins unrelated to disease, such as the Src homology 3 (SH3) domain of the p58α subunit of bovine phosphatidyl-inositol-3′-kinase (PI3-SH3), can be converted in vitro into assemblies with structural and cytotoxic properties similar to those of pathological aggregates. By contrast, homologous proteins, such as α-spectrin-SH3, lack the capability of forming amyloid fibrils at a measurable rate under any of the conditions we have so far examined. However, transplanting a small sequence stretch (6 aa) from PI3-SH3 to α-spectrin-SH3, comprising residues of the diverging turn and adjacent RT loop, creates an amyloidogenic protein closely similar in its behavior to the original PI3-SH3. Analysis of specific PI3-SH3 mutants further confirms the involvement of this region in conferring amyloidogenic properties to this domain. Moreover, the inclusion in this stretch of two consensus residues favored in SH3 sequences substantially inhibits aggregation. These findings show that short specific amino acid stretches can act as mediators or facilitators in the incorporation of globular proteins into amyloid structures, and they support the suggestion that natural protein sequences have evolved in part to code for structural characteristics other than those included in the native fold, such as avoidance of aggregation. PMID:15123800

  6. Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case.

    PubMed

    Ventura, Salvador; Zurdo, Jesús; Narayanan, Saravanakumar; Parreño, Matilde; Mangues, Ramón; Reif, Bernd; Chiti, Fabrizio; Giannoni, Elisa; Dobson, Christopher M; Aviles, Francesc X; Serrano, Luis

    2004-05-11

    Protein misfolding and deposition underlie an increasing number of debilitating human disorders. We have shown that model proteins unrelated to disease, such as the Src homology 3 (SH3) domain of the p58alpha subunit of bovine phosphatidyl-inositol-3'-kinase (PI3-SH3), can be converted in vitro into assemblies with structural and cytotoxic properties similar to those of pathological aggregates. By contrast, homologous proteins, such as alpha-spectrin-SH3, lack the capability of forming amyloid fibrils at a measurable rate under any of the conditions we have so far examined. However, transplanting a small sequence stretch (6 aa) from PI3-SH3 to alpha-spectrin-SH3, comprising residues of the diverging turn and adjacent RT loop, creates an amyloidogenic protein closely similar in its behavior to the original PI3-SH3. Analysis of specific PI3-SH3 mutants further confirms the involvement of this region in conferring amyloidogenic properties to this domain. Moreover, the inclusion in this stretch of two consensus residues favored in SH3 sequences substantially inhibits aggregation. These findings show that short specific amino acid stretches can act as mediators or facilitators in the incorporation of globular proteins into amyloid structures, and they support the suggestion that natural protein sequences have evolved in part to code for structural characteristics other than those included in the native fold, such as avoidance of aggregation.

  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. 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.

  10. 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.

  11. 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. Copyright 2010 Elsevier Inc. All rights reserved.

  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. 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.

  15. 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. © 2016 Wiley Periodicals, Inc.

  16. 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.

  17. 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+.

  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. Solution stability and variability in a simple model of globular proteins.

    PubMed

    Sear, Richard P

    2004-01-08

    It is well known among molecular biologists that proteins with a common ancestor and that perform the same function in similar organisms, can have rather different amino-acid sequences. Mutations have altered the amino-acid sequences without affecting the function. A simple model of a protein in which the interactions are encoded by sequences of bits is introduced, and used to study how mutations can change these bits, and hence the interactions, while maintaining the stability of the protein solution. This stability is a simple minimal requirement on our model proteins which mimics part of the requirement on a real protein to be functional. The properties of our model protein, such as its second virial coefficient, are found to vary significantly from one model protein to another. It is suggested that this may also be the case for real proteins in vivo. (c) 2004 American Institute of Physics

  20. 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.

  1. 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.

  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. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

    SciTech Connect

    Miao, Yinglong; Hong, Liang; Yi, Zheng; Smith, Jeremy C.

    2013-07-16

    A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Furthermore, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.

  4. Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein.

    PubMed

    Gianni, Stefano; Camilloni, Carlo; Giri, Rajanish; Toto, Angelo; Bonetti, Daniela; Morrone, Angela; Sormanni, Pietro; Brunori, Maurizio; Vendruscolo, Michele

    2014-09-30

    Folding and function may impose different requirements on the amino acid sequences of proteins, thus potentially giving rise to conflict. Such a conflict, or frustration, can result in the formation of partially misfolded intermediates that can compromise folding and promote aggregation. We investigate this phenomenon by studying frataxin, a protein whose normal function is to facilitate the formation of iron-sulfur clusters but whose mutations are associated with Friedreich's ataxia. To characterize the folding pathway of this protein we carry out a Φ-value analysis and use the resulting structural information to determine the structure of the folding transition state, which we then validate by a second round of rationally designed mutagenesis. The analysis of the transition-state structure reveals that the regions involved in the folding process are highly aggregation-prone. By contrast, the regions that are functionally important are partially misfolded in the transition state but highly resistant to aggregation. Taken together, these results indicate that in frataxin the competition between folding and function creates the possibility of misfolding, and that to prevent aggregation the amino acid sequence of this protein is optimized to be highly resistant to aggregation in the regions involved in misfolding.

  5. 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

  6. Investigating plausible mechanisms for the photo-induced partial unfolding of a globular protein

    NASA Astrophysics Data System (ADS)

    Parker, James E.

    Two hypotheses are proposed to explain the photo-induced unfolding of β-lactoglobulin (BLG) that occurs when non-covalently bound to a dye molecule, meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP), and illuminated by a laser in the post-Tanford transition configuration. The first involves a photo-induced electron transfer from the porphyrin to the protein. The second involves the production of kynurenine by singlet oxygen that is generated during photo-excitation of the porphyrin. To evaluate these hypotheses, a series of computational and experimental results have been combined to establish the physical state of the BLG-TSPP complex and to estimate the likelihood of a post-irradiation event to initiate the partial unfolding. Determining the binding site location is crucial to establish the position of the photo-induced events and the likely end-product. A study of the vibronic state of the BLG-TSPP complex using resonant Raman and absorption spectroscopy coupled with density functional theory (DFT) and docking simulations is used to estimate the location of the binding site. Once the binding site is found, molecular dynamics simulations of the post-irradiation event relaxations in the protein are used to estimate the resulting secondary structure. This structure is compared to experimental estimates of the secondary structure of the unfolded protein to determine which hypothesis is the most likely mechanism to explain the unfolding.

  7. Evolution of the internal dynamics of two globular proteins from dry powder to solution.

    PubMed Central

    Pérez, J; Zanotti, J M; Durand, D

    1999-01-01

    Myoglobin and lysozyme picosecond internal dynamics in solution is compared to that in hydrated powders by quasielastic incoherent neutron scattering. This technique is sensitive to the motions of the nonexchangeable hydrogen atoms in a sample. Because these are homogeneously distributed throughout the protein structure, the average dynamics of the protein is described. We first propose an original data treatment to deal with the protein global motions in the case of solution samples. The validity of this treatment is checked by comparison with classical measurements of the diffusion constants. The evolution with the scattering vector of the width and relative contribution of the quasielastic component was then used to derive information on the amount of local diffusive motions and their characteristic average relaxation time. From dry powder to coverage by one water layer, the surface side chains progressively acquire the possibility to diffuse locally. On subsequent hydration, the main effect of water is to improve the rate of these diffusive motions. Motions with higher average amplitude occur in solution, about three times more than for a hydrated powder at complete coverage, with a shorter average relaxation time, approximately 4.5 ps compared to 9.4 ps for one water monolayer. PMID:10388771

  8. 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

  9. 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

  10. Effect of interfacial viscoelasticity on the bulk linear viscoelastic moduli of globular protein solutions

    NASA Astrophysics Data System (ADS)

    Zhang, Zhenhuan; Barman, Sourav; Christopher, Gordon F.

    2014-05-01

    The role of interfacial rheology on the bulk linear viscoelastic moduli of low concentration bovine albumin solutions is probed. Previously reported soft gel properties of these systems were attributed to either protein aggregation or organization within the bulk. Instead, these behaviors are shown to be attributable to the measurement error caused by interfacial rheology due to adsorption of bovine serum albumin to the air and water interface. Even at low bulk concentrations, fast interfacial adsorption results in erroneous measurements. When these effects are removed, the solutions are viscous dominated with a dynamic viscosity slightly larger than water.

  11. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Hydration and stability of some globular proteins in the nonpolar medium in the presence of phosphatidilholine

    NASA Astrophysics Data System (ADS)

    Klimovich, Valeriy M.; Gulay, I. S.

    2000-12-01

    Intention of present work is research the influence of non- polar medium and phosphatidilholine on stability of the macromolecules and hydration of cytohrom-C, tripsine and insulin by use of methods laser Raman and Infrared spectroscopy and isotope H/D exchange. It is shown, that the non-polar environment causes convertible changes of spatial pattern of macromolecules a protein degree of order of macromolecules as a result of which is increased. The presence of water at a system results in a converse effect. At interaction of phosphatidilcholin with the protondonors groups a protein will derivate complexes with a hydrogen bonds. Thereof quantity of aminoacidic oddments which are generatix a polar circuit of a plaited layer is augmented. The outcomes of the analysis of bands of compound tone of water testify to presence in a system of three varieties of water clusters distinguished by frequencies of libration oscillations. It is suspected, that the hydrophobic environment can cause reduction of movability of molecules of water in different clusters.

  13. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures.

    PubMed

    Eswar, N; Ramakrishnan, C

    2000-04-01

    A total of 19 835 polar residues from a data set of 250 non-homologous and highly resolved protein crystal structures were used to identify side-chain main-chain (SC-MC) hydrogen bonds. The ratio of the number of SC-MC hydrogen bonds to the total number of polar residues is close to 1:2, indicating the ubiquitous nature of such hydrogen bonds. Close to 56% of the SC-MC hydrogen bonds are local involving side-chain acceptor/donor ('i') and a main-chain donor/acceptor within the window i-5 to i+5. These short-range hydrogen bonds form well defined conformational motifs characterized by specific combinations of backbone and side-chain torsion angles. (a) The Ser/Thr residues show the greatest preference in forming intra-helical hydrogen bonds between the atoms O(gamma)(i) and O(i-4). More than half the examples of such hydrogen bonds are found at the middle of alpha-helices rather than at their ends. The most favoured motif of these examples is alpha(R)alpha(R)alpha(R)alpha(R)(g(-)). (b) These residues also show great preference to form hydrogen bonds between O(gamma)(i) and O(i-3), which are closely related to the previous type and though intra-helical, these hydrogen bonds are more often found at the C-termini of helices than at the middle. The motif represented by alpha(R)alpha(R)alpha(R)alpha(R)(g(+)) is most preferred in these cases. (c) The Ser, Thr and Glu are the most frequently found residues participating in intra-residue hydrogen bonds (between the side-chain and main-chain of the same residue) which are characterized by specific motifs of the form beta(g(+)) for Ser/Thr residues and alpha(R)(g(-)g(+)t) for Glu/Gln. (d) The side-chain acceptor atoms of Asn/Asp and Ser/Thr residues show high preference to form hydrogen bonds with acceptors two residues ahead in the chain, which are characterized by the motifs beta (tt')alphaR and beta(t)alpha(R), respectively. These hydrogen bonded segments, referred to as Asx turns, are known to provide stability to type I

  14. The SLUGGS survey: dark matter fractions at large radii and assembly epochs of early-type galaxies from globular cluster kinematics

    NASA Astrophysics Data System (ADS)

    Alabi, Adebusola B.; Forbes, Duncan A.; Romanowsky, Aaron J.; Brodie, Jean P.; Strader, Jay; Janz, Joachim; Usher, Christopher; Spitler, Lee R.; Bellstedt, Sabine; Ferré-Mateu, Anna

    2017-07-01

    We use globular cluster kinematics data, primarily from the SAGES Legacy Unifying Globulars and GalaxieS (SLUGGS) survey, to measure the dark matter fraction (fDM) and the average dark matter density (<ρDM>) within the inner 5 effective radii (Re) for 32 nearby early-type galaxies (ETGs) with stellar mass log (M*/M⊙) ranging from 10.1 to 11.8. We compare our results with a simple galaxy model based on scaling relations as well as with cosmological hydrodynamical simulations where the dark matter profile has been modified through various physical processes. We find a high fDM (≥0.6) within 5 Re in most of our sample, which we interpret as a signature of a late mass assembly history that is largely devoid of gas-rich major mergers. However, around log (M*/M⊙) ˜ 11, there is a wide range of fDM which may be challenging to explain with any single cosmological model. We find tentative evidence that lenticulars (S0s), unlike ellipticals, have mass distributions that are similar to spiral galaxies, with decreasing fDM within 5 Re as galaxy luminosity increases. However, we do not find any difference between the <ρDM> of S0s and ellipticals in our sample, despite the differences in their stellar populations. We have also used <ρDM> to infer the epoch of halo assembly (z ˜ 2-4). By comparing the age of their central stars with the inferred epoch of halo formation, we are able to gain more insight into their mass assembly histories. Our results suggest a fundamental difference in the dominant late-phase mass assembly channel between lenticulars and elliptical galaxies.

  15. 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

  16. Effects of heating rate and pH on fracture and water-holding properties of globular protein gels as explained by micro-phase separation.

    PubMed

    Leksrisompong, Phanin N; Lanier, Tyre C; Foegeding, E Allen

    2012-02-01

    The effect of heating rate and pH on fracture properties and held water (HW) of globular protein gels was investigated. The study was divided into 2 experiments. In the 1st experiment, whey protein isolate (WPI) and egg white protein (EWP) gels were formed at pH 4.5 and 7.0 using heating rates ranging from 0.1 to 35 °C/min and holding times at 80 °C up to 240 min. The 2nd experiment used one heating condition (80 °C for 60 min) and probed in detail the pH range of 4.5 to 7.0 for EWP gels. Fracture properties of gels were measured by torsional deformation and HW was measured as the amount of fluid retained after a mild centrifugation. Single or micro-phase separated conditions were determined by confocal laser scanning microscopy. The effect of heating rate on fracture properties and HW of globular protein gels can be explained by phase stability of the protein dispersion and total thermal input. Minimal difference in fracture properties and HW of EWP gels at pH 4.5 compared with pH 7.0 were observed while WPI gels were stronger and had higher HW at pH 7.0 as compared to 4.5. This was due to a mild degree of micro-phase separation of EWP gels across the pH range whereas WPI gels only showed an extreme micro-phase separation in a narrow pH range. In summary, gel formation and physical properties of globular protein gels can be explained by micro-phase separation. The effect of heating conditions on hardness and water-holding properties of protein gels is explained by the relative percentage of micro-phase separated proteins. Heating rates that are too rapid require additional holding time at the end-point temperature to allow for full network development. Increase in degree of micro-phase separation decreases the ability for protein gels to hold water. © 2012 Institute of Food Technologists®

  17. 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

  18. Acid-induced cold gelation of globular proteins: effects of protein aggregate characteristics and disulfide bonding on rheological properties.

    PubMed

    Alting, Arno C; Weijers, Mireille; de Hoog, Els H A; van de Pijpekamp, Anne M; Cohen Stuart, Martien A; Hamer, Rob J; de Kruif, Cornelis G; Visschers, Ronald W

    2004-02-11

    The process of cold gelation of ovalbumin and the properties of the resulting cold-set gels were compared to those of whey protein isolate. Under the chosen heating conditions, most protein was organized in aggregates. For both protein preparations, the aggregates consisted of covalently linked monomers. Both types of protein aggregates had comparable numbers of thiol groups exposed at their surfaces but had clearly different shapes. During acid-induced gelation, the characteristic ordering caused by the repulsive character disappeared and was replaced by a random distribution. This process did not depend on aggregate characteristics and probably applies to any type of protein aggregate. Covalent bonds are the main determinants of the gel hardness. The formation of additional disulfide bonds during gelation depended on the number and accessibility of thiol groups and disulfide bonds in the molecule and was found to clearly differ between the proteins studied. However, upon blocking of the thiol groups, long fibrillar structures of ovalbumin contribute significantly to gel hardness, demonstrating the importance of aggregate shape.

  19. 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.

  20. Structure-function relationship in the globular type III antifreeze protein: identification of a cluster of surface residues required for binding to ice.

    PubMed Central

    Chao, H.; Sönnichsen, F. D.; DeLuca, C. I.; Sykes, B. D.; Davies, P. L.

    1994-01-01

    Antifreeze proteins (AFPs) depress the freezing point of aqueous solutions by binding to and inhibiting the growth of ice. Whereas the ice-binding surface of some fish AFPs is suggested by their linear, repetitive, hydrogen bonding motifs, the 66-amino-acid-long Type III AFP has a compact, globular fold without any obvious periodicity. In the structure, 9 beta-strands are paired to form 2 triple-stranded antiparallel sheets and 1 double-stranded antiparallel sheet, with the 2 triple sheets arranged as an orthogonal beta-sandwich (Sönnichsen FD, Sykes BD, Chao H, Davies PL, 1993, Science 259:1154-1157). Based on its structure and an alignment of Type III AFP isoform sequences, a cluster of conserved, polar, surface-accessible amino acids (N14, T18, Q44, and N46) was noted on and around the triple-stranded sheet near the C-terminus. At 3 of these sites, mutations that switched amide and hydroxyl groups caused a large decrease in antifreeze activity, but amide to carboxylic acid changes produced AFPs that were fully active at pH 3 and pH 6. This is consistent with the observation that Type III AFP is optimally active from pH 2 to pH 11. At a concentration of 1 mg/mL, Q44T, N14S, and T18N had 50%, 25%, and 10% of the activity of wild-type antifreeze, respectively. The effects of the mutations were cumulative, such that the double mutant N14S/Q44T had 10% of the wild-type activity and the triple mutant N14S/T18N/Q44T had no activity. All mutants with reduced activity were shown to be correctly folded by NMR spectroscopy. Moreover, a complete characterization of the triple mutant by 2-dimensional NMR spectroscopy indicated that the individual and combined mutations did not significantly alter the structure of these proteins. These results suggest that the C-terminal beta-sheet of Type III AFP is primarily responsible for antifreeze activity, and they identify N14, T18, and Q44 as key residues for the AFP-ice interaction. PMID:7849594

  1. 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.

  2. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. 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.

  4. 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.

  5. The Second Receptor Binding Site of the Globular Head of the Newcastle Disease Virus Hemagglutinin-Neuraminidase Activates the Stalk of Multiple Paramyxovirus Receptor Binding Proteins To Trigger Fusion

    PubMed Central

    Salah, Zuhair; DeVito, Ilaria; Talekar, Aparna; Palmer, Samantha G.; Xu, Rui; Wilson, Ian A.

    2012-01-01

    The hemagglutinin-neuraminidase (HN) protein of paramyxoviruses carries out three distinct activities contributing to the ability of HN to promote viral fusion and entry: receptor binding, receptor cleavage (neuraminidase), and activation of the fusion protein. The relationship between receptor binding and fusion triggering functions of HN are not fully understood. For Newcastle disease virus (NDV), one bifunctional site (site I) on HN′s globular head can mediate both receptor binding and neuraminidase activities, and a second site (site II) in the globular head is also capable of mediating receptor binding. The receptor analog, zanamivir, blocks receptor binding and cleavage activities of NDV HN′s site I while activating receptor binding by site II. Comparison of chimeric proteins in which the globular head of NDV HN is connected to the stalk region of either human parainfluenza virus type 3 (HPIV3) or Nipah virus receptor binding proteins indicates that receptor binding to NDV HN site II not only can activate its own fusion (F) protein but can also activate the heterotypic fusion proteins. We suggest a general model for paramyxovirus fusion activation in which receptor engagement at site II plays an active role in F activation. PMID:22438532

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. Globular Clusters for Faint Galaxies

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2017-07-01

    The origin of ultra-diffuse galaxies (UDGs) has posed a long-standing mystery for astronomers. New observations of several of these faint giants with the Hubble Space Telescope are now lending support to one theory.Faint-Galaxy MysteryHubble images of Dragonfly 44 (top) and DFX1 (bottom). The right panels show the data with greater contrast and extended objects masked. [van Dokkum et al. 2017]UDGs large, extremely faint spheroidal objects were first discovered in the Virgo galaxy cluster roughly three decades ago. Modern telescope capabilities have resulted in many more discoveries of similar faint galaxies in recent years, suggesting that they are a much more common phenomenon than we originally thought.Despite the many observations, UDGs still pose a number of unanswered questions. Chief among them: what are UDGs? Why are these objects the size of normal galaxies, yet so dim? There are two primary models that explain UDGs:UDGs were originally small galaxies, hence their low luminosity. Tidal interactions then puffed them up to the large size we observe today.UDGs are effectively failed galaxies. They formed the same way as normal galaxies of their large size, but something truncated their star formation early, preventing them from gaining the brightness that we would expect for galaxies of their size.Now a team of scientists led by Pieter van Dokkum (Yale University) has made some intriguing observations with Hubble that lend weight to one of these models.Globulars observed in 16 Coma-cluster UDGs by Hubble. The top right panel shows the galaxy identifications. The top left panel shows the derived number of globular clusters in each galaxy. [van Dokkum et al. 2017]Globulars GaloreVan Dokkum and collaborators imaged two UDGs with Hubble: Dragonfly 44 and DFX1, both located in the Coma galaxy cluster. These faint galaxies are both smooth and elongated, with no obvious irregular features, spiral arms, star-forming regions, or other indications of tidal interactions

  11. 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.

  12. 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

  13. 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

  14. Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins.

    PubMed

    Bahadur, Ranjit Prasad; Chakrabarti, Pinak

    2009-12-28

    Setting the rules for the identification of a stable conformation of a protein is of utmost importance for the efficient generation of structures in computer simulation. For structure prediction, a considerable number of possible models are generated from which the best model has to be selected. Two scoring functions, Rs and Rp, based on the consideration of packing of residues, which indicate if the conformation of an amino acid sequence is native-like, are presented. These are defined using the solvent accessible surface area (ASA) and the partner number (PN) (other residues that are within 4.5 A) of a particular residue. The two functions evaluate the deviation from the average packing properties (ASA or PN) of all residues in a polypeptide chain corresponding to a model of its three-dimensional structure. While simple in concept and computationally less intensive, both the functions are at least as efficient as any other energy functions in discriminating the native structure from decoys in a large number of standard decoy sets, as well as on models submitted for the targets of CASP7. Rs appears to be slightly more effective than Rp, as determined by the number of times the native structure possesses the minimum value for the function and its separation from the average value for the decoys. Two parameters, Rs and Rp, are discussed that can very efficiently recognize the native fold for a sequence from an ensemble of decoy structures. Unlike many other algorithms that rely on the use of composite scoring function, these are based on a single parameter, viz., the accessible surface area (or the number of residues in contact), but still able to capture the essential attribute of the native fold.

  15. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs.

    PubMed

    Ikeda, Kazuyoshi; Tomii, Kentaro; Yokomizo, Tsuyoshi; Mitomo, Daisuke; Maruyama, Keiichiro; Suzuki, Shinya; Higo, Junichi

    2005-05-01

    Analysis of the conformational distribution of polypeptide segments in a conformational space is the first step for understanding a principle of structural diversity of proteins. Here, we present a statistical analysis of protein local structures based on interatomic C(alpha) distances. Using principal component analysis (PCA) on the intrasegment C(alpha)-C(alpha) atomic distances, the conformational space of protein segments, which we call the protein segment universe, has been visualized, and three essential coordinate axes, suitable for describing the universe, have been identified. Three essential axes specified radius of gyration, structural symmetry, and separation of hairpin structures from other structures. Among the segments of arbitrary length, 6-22 residues long, the conservation of those axes was uncovered. Further application of PCA to the two largest clusters in the universe revealed local structural motifs. Although some of motifs have already been reported, we identified a possibly novel strand motif. We also showed that a capping box, which is one of the helix capping motifs, was separated into independent subclusters based on the C(alpha) geometry. Implications of the strand motif, which may play a role for protein-protein interaction, are discussed. The currently proposed method is useful for not only mapping the immense universe of protein structures but also identification of structural motifs.

  16. 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.

  17. 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.

  18. 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

  19. Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

    PubMed

    Fačkovec, Boris; Vondrášek, Jiří

    2012-10-25

    Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

  20. 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.

  1. Globular Clusters as Cradles of Life and Advanced Civilizations

    NASA Astrophysics Data System (ADS)

    Di Stefano, Rosanne; Ray, Alak

    2016-01-01

    Globular clusters are bound groups of about a million stars and stellar remnants. They are old, largely isolated, and very dense. We consider what each of these special features can mean for the development of life, the evolution of intelligent life, and the long-term survival of technological civilizations. We find that, if they house planets, globular clusters provide ideal environments for advanced civilizations that can survive over long times. We therefore propose methods to search for planets in globular clusters. If planets are found and if our arguments are correct, searches for intelligent life are most likely to succeed when directed toward globular clusters. Globular clusters may be the first places in which distant life is identified in our own or in external galaxies.

  2. Large Proteins Have a Great Tendency to Aggregate but a Low Propensity to Form Amyloid Fibrils

    PubMed Central

    Ramshini, Hassan; Parrini, Claudia; Relini, Annalisa; Zampagni, Mariagioia; Mannini, Benedetta; Pesce, Alessandra; Saboury, Ali Akbar; Nemat-Gorgani, Mohsen; Chiti, Fabrizio

    2011-01-01

    The assembly of soluble proteins into ordered fibrillar aggregates with cross-β structure is an essential event of many human diseases. The polypeptides undergoing aggregation are generally small in size. To explore if the small size is a primary determinant for the formation of amyloids under pathological conditions we have created two databases of proteins, forming amyloid-related and non-amyloid deposits in human diseases, respectively. The size distributions of the two protein populations are well separated, with the systems forming non-amyloid deposits appearing significantly larger. We have then investigated the propensity of the 486-residue hexokinase-B from Saccharomyces cerevisiae (YHKB) to form amyloid-like fibrils in vitro. This size is intermediate between the size distributions of amyloid and non-amyloid forming proteins. Aggregation was induced under conditions known to be most effective for amyloid formation by normally globular proteins: (i) low pH with salts, (ii) pH 5.5 with trifluoroethanol. In both situations YHKB aggregated very rapidly into species with significant β-sheet structure, as detected using circular dichroism and X-ray diffraction, but a weak Thioflavin T and Congo red binding. Moreover, atomic force microscopy indicated a morphology distinct from typical amyloid fibrils. Both types of aggregates were cytotoxic to human neuroblastoma cells, as indicated by the MTT assay. This analysis indicates that large proteins have a high tendency to form toxic aggregates, but low propensity to form regular amyloid in vivo and that such a behavior is intrinsically determined by the size of the protein, as suggested by the in vitro analysis of our sample protein. PMID:21249193

  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. 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.

  5. 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.

  6. 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

  7. 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.

  8. Thermal motion in proteins: Large effects on the time-averaged interaction energies

    SciTech Connect

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

    2016-03-15

    As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

  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. Glycosylations in the globular head of the hemagglutinin protein modulate the virulence and antigenic properties of the H1N1 influenza viruses

    PubMed Central

    Medina, Rafael A.; Stertz, Silke; Manicassamy, Balaji; Zimmermann, Petra; Sun, Xiangjie; Albrecht, Randy A.; Uusi-Kerttula, Hanni; Zagordi, Osvaldo; Belshe, Robert B.; Frey, Sharon E.; Eggink, Dirk; Tumpey, Terrence M.; García-Sastre, Adolfo

    2014-01-01

    The global spread of the 2009 pandemic H1N1 (pH1N1) virus in humans increases the likelihood that this influenza virus strain could undergo antigenic drift in the coming years. Previous seasonal H1N1 and H3N2 influenza strains acquired additional glycosylations in the globular head of their hemagglutinin (HA) proteins as they evolved over time; these are believed to shield antigenically relevant regions. We used influenza A/Netherlands/602/2009 recombinant (rpH1N1) viruses to which we added additional HA glycosylation sites reflecting their temporal appearance in previous seasonal H1N1 viruses. Additional glycosylations resulted in substantial attenuation in mice and ferrets, while deleting HA glycosylation sites from a pre-pandemic 1991 seasonal H1N1 influenza virus resulted in increased pathogenicity in mice. Sera from mice infected with wild type (WT) rpH1N1 virus showed a considerable loss of HA inhibitory (HI) activity against rpH1N1 viruses glycosylated at sites 144 or 144-172, indicating that the polyclonal antibody response elicited by WT rpH1N1 HA seems to be directed against an immunodominant region, likely site Sa, shielded by glycosylation at 144. Sera from humans vaccinated with the pH1N1 inactivated vaccine also showed reduced activity against the 144 and 144-172 mutant viruses. Remarkably, the HI activity of sera from virus-infected mice demonstrated that glycosylation at position 144 resulted in the induction of a broader polyclonal response able to cross-neutralize all WT and glycosylation mutant pH1N1 viruses. Mice infected with a recent seasonal virus in which glycosylation sites 71, 142 and 177 were removed, elicited antibodies that protected against challenge with the antigenically distant pH1N1 virus. Thus, acquisition of glycosylation sites in the HA of H1N1 human influenza viruses not only affects their pathogenicity and ability to escape from polyclonal antibodies elicited by previous influenza virus strains, but also their ability to

  11. 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.

  12. Mass Segregation in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Fregeau, J. M.; Joshi, K. J.; Portegies Zwart, S. F.; Rasio, F. A.

    2002-05-01

    We present the results of a new study of mass segregation in two-component star clusters, based on a large number of numerical N-body simulations using our recently developed dynamical Monte Carlo code. Specifically, we follow the dynamical evolution of clusters containing stars with individual masses m1 as well as a tracer population of objects with individual masses m2. We consider both light tracers (μ≡m2/m1<1) and heavy tracers (μ>1) and a variety of King model initial conditions. In all of our simulations we use a realistically large number of stars for globular clusters, N=105, but we ignore the effects of binaries and stellar evolution. For heavy tracers, which could represent stellar remnants such as neutron stars or black holes in a globular cluster, we characterize in a variety of ways the tendency for these objects to concentrate in or near the cluster core. In agreement with simple theoretical arguments, we find that the characteristic time for this mass segregation process varies as 1/μ. For models with very light tracers (μ<~10-2), which could represent free-floating planets or brown dwarfs, we find the expected depletion of light objects in the cluster core but also sometimes a significant enhancement in the halo. That is, for some initial conditions, the number density of light objects in the cluster halo increases over time, in spite of the higher overall evaporation rate of lighter objects through the tidal boundary. Using these results along with a simplified initial mass function, we estimate the optical depth to gravitational microlensing by planetary mass objects or brown dwarfs in typical globular clusters. For some initial conditions, the optical depth in the halo owing to very low mass objects could be much greater than that of luminous stars. If we apply our results to M22, using the recent null detection of Sahu, Anderson, & King, we find an upper limit of ~25% at the 63% confidence level for the current mass fraction of M22 in the

  13. 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.

  14. 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

  15. 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.

  16. Chemical Abundances of Giants in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Gratton, Raffaele G.; Bragaglia, Angela; Carretta, Eugenio; D'Orazi, Valentina; Lucatello, Sara

    A large fraction of stars form in clusters. According to a widespread paradigma, stellar clusters are prototypes of single stellar populations. According to this concept, they formed on a very short time scale, and all their stars share the same chemical composition. Recently it has been understood that massive stellar clusters (the globular clusters) rather host various stellar populations, characterized by different chemical composition: these stellar populations have also slightly different ages, stars of the second generations being formed from the ejecta of part of those of an earlier one. Furthermore, it is becoming clear that the efficiency of the process is quite low: many more stars formed within this process than currently present in the clusters. This implies that a significant, perhaps even dominant fraction of the ancient population of galaxies formed within the episodes that lead to formation the globular clusters.

  17. 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.

  18. 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.

  19. 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)

  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. 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.

  2. 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

  3. 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

  4. 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.

  5. The Newly-Discovered Outer Halo Globular Cluster System of M31

    NASA Astrophysics Data System (ADS)

    Mackey, D.; Huxor, A.; Ferguson, A.

    2012-08-01

    In this contribution we describe the discovery of a large number of globular clusters in the outer halo of M31 from the Pan-Andromeda Archaeological Survey (PAndAS). New globular clusters have also been found in the outskirts of M33, and NGC 147 and 185. Many of the remote M31 clusters are observed to preferentially project onto tidal debris streams in the stellar halo, suggesting that much of the outer M31 globular cluster system has been assembled via the accretion of satellite galaxies. We briefly discuss the global properties of the M31 halo globular cluster system.

  6. 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.

  7. 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.

  8. Globular clusters with Gaia

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

    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 majority 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 per cent 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 unprecedented quality, cluster masses will be determined to ≃10 per cent 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 per cent errors on the absolute photometric calibration.

  9. 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.

  10. 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.

  11. Dark Matter Halos in Galaxies and Globular Cluster Populations

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    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 GCS/M h (total mass in globular clusters, divided by halo mass) is essentially constant at langηrang ~ 4 × 10-5, 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 langηrang indicates that the halo masses of the Milky Way and M31 are (1.2 ± 0.5) × 1012 M ⊙ and (3.9 ± 1.8) × 1012 M ⊙, respectively.

  12. The youngest globular clusters

    NASA Astrophysics Data System (ADS)

    Beck, Sara

    2015-11-01

    It is likely that all stars are born in clusters, but most clusters are not bound and disperse. None of the many protoclusters in our Galaxy are likely to develop into long-lived bound clusters. The super star clusters (SSCs) seen in starburst galaxies are more massive and compact and have better chances of survival. The birth and early development of SSCs takes place deep in molecular clouds, and during this crucial stage the embedded clusters are invisible to optical or UV observations but are studied via the radio-infrared supernebulae (RISN) they excite. We review observations of embedded clusters and identify RISN within 10 Mpc whose exciting clusters have ≈ 106 M⊙ or more in volumes of a few pc3 and which are likely to not only survive as bound clusters, but to evolve into objects as massive and compact as Galactic globulars. These clusters are distinguished by very high star formation efficiency η, at least a factor of 10 higher than the few percent seen in the Galaxy, probably due to the violent disturbances their host galaxies have undergone. We review recent observations of the kinematics of the ionized gas in RISN showing outflows through low-density channels in the ambient molecular cloud; this may protect the cloud from feedback by the embedded H II region.

  13. 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.

  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. 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.

  16. 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.

  17. Photoswitchable red fluorescent protein with a large Stokes shift

    PubMed Central

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

    2014-01-01

    SUMMARY Subclass of fluorescent proteins, large Stokes shift fluorescent proteins, is characterized by their increased spread between the excitation and emission maxima. Here we report a photoswitchable variant of a red fluorescent protein with a large Stokes shift, PSLSSmKate, which initially exhibits excitation/emission at 445/622 nm, but irradiation with violet light photoswitches PSLSSmKate into a common red form with excitation/emission at 573/621 nm. We characterize spectral, photophysical and biochemical properties of PSLSSmKate in vitro and in mammalian cells, and determine its crystal structure in the large Stokes shift form. Mass-spectrometry, mutagenesis and spectroscopic analysis of PSLSSmKate allow us to propose molecular mechanisms for the large Stokes shift, pH dependence and light-induced chromophore transformation. We demonstrate applicability of PSLSSmKate to superresolution PALM 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. PMID:25242289

  18. Large-scale mapping of human protein-protein interactions by mass spectrometry.

    PubMed

    Ewing, Rob M; Chu, Peter; Elisma, Fred; Li, Hongyan; Taylor, Paul; Climie, Shane; McBroom-Cerajewski, Linda; Robinson, Mark D; O'Connor, Liam; Li, Michael; Taylor, Rod; Dharsee, Moyez; Ho, Yuen; Heilbut, Adrian; Moore, Lynda; Zhang, Shudong; Ornatsky, Olga; Bukhman, Yury V; Ethier, Martin; Sheng, Yinglun; Vasilescu, Julian; Abu-Farha, Mohamed; Lambert, Jean-Philippe; Duewel, Henry S; Stewart, Ian I; Kuehl, Bonnie; Hogue, Kelly; Colwill, Karen; Gladwish, Katharine; Muskat, Brenda; Kinach, Robert; Adams, Sally-Lin; Moran, Michael F; Morin, Gregg B; Topaloglou, Thodoros; Figeys, Daniel

    2007-01-01

    Mapping protein-protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein-protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24,540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein-protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations.

  19. 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.

  20. Dynamical evolution of globular clusters in dark matter halos

    NASA Astrophysics Data System (ADS)

    Breen, Phil; Varri, Anna Lisa; Penarrubia, Jorge; Heggie, Douglas C.

    2017-06-01

    The formation of globular clusters in a cosmological context is a topical open problem. One possible formation scenario is that globular clusters have formed in their own dark matter halos, and, as a result, some clusters may have retained it to the present day. In such a case, collisional processes taking place in the central regions of globulars may lead to the formation of a tenuous stellar envelope extending far beyond the tidal boundary of the parent cluster.The synergy between the astrometric mission Gaia and forthcoming multi-object spectrographs such as WEAVE will allow us to explore, with unprecedented accuracy, the outer regions of selected Galactic globular clusters, therefore it is particularly timely to consider to what extent the presence of dark matter is consistent with their dynamics and structure at large distances from the cluster centre.Driven by these motivations, we present the results of a series of direct N-body simulations where globular clusters have been evolved self-consistently in a static dark matter potential. Special attention will be given to the exploration of the effects of the dark halo on the traditional phases of the long-term evolution of collisional systems and the dynamical interplay with other fundamental physical ingredients, such as stellar-mass black holes, will be discussed.

  1. Extremely α -Enriched Globular Clusters in Early-Type Galaxies

    NASA Astrophysics Data System (ADS)

    Puzia, T. H.; Kissler-Patig, M.; Goudfrooij, P.

    2005-12-01

    We compare [α /Fe], metallicity, and age distributions of globular clusters in elliptical, lenticular, and spiral galaxies, which we derive from Lick line index measurements. We find a large number of globular clusters in elliptical galaxies that reach significantly higher [α /Fe] values ([α /Fe] >0.5) than clusters in lenticular and spiral galaxies. Most of these highly α -enriched globular clusters are old (t>8 Gyr) and exhibit relatively high metallicities up to solar values. A comparison with supernova yield models suggests that the progenitor gas clouds of these globular clusters were predominantly enriched by massive stars (⪆ 20 M⊙) with little contribution from lower-mass stars. The measured [α /Fe] ratios are also consistent with yields of very massive pair-instability supernovae ( ˜130-190 M⊙). This implies that the chemical enrichment of the progenitor gas was completed on extremely short timescales of the order of a few Myr. Given the lower [α /Fe] ratios of the diffuse stellar population in early-type galaxies, our results suggest that the extremely α -enhanced globular clusters are members of the the very first generation of star clusters formed, and that their formation epochs likely predate the formation of the majority of stars in giant early-type galaxies.

  2. 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.

  3. Integrated photometry of globular clusters in the Vilnius system

    NASA Astrophysics Data System (ADS)

    Zdanavicius, K. V.

    1983-02-01

    Integrated color indices measured in the Vilnius photometric system and color excesses are given for 39 globular clusters. The integrated spectral type is not a sufficient criterion for globular clusters to have identical intrinsic colors. A study is made of the relation between the integrated color indices and parameters of the H-R diagram: the Dickens morphological type D of the horizontal branch and the slope S of the giant branch. The integrated colors of clusters with a blue horizontal branch show no correlation with either D or S. The remaining clusters have large color indices mainly because their stars are redistributed along the horizontal branch.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Globular cluster systems in spiral galaxies

    NASA Astrophysics Data System (ADS)

    Nantais, Julie Beth

    We have performed a comprehensive spectroscopic and photometric analysis of the M81 globular cluster system, using Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) imaging in the B, V, and I bands and 74 globular cluster spectra from Hectospec at the MMT. We have also performed a small spectroscopic study of the NGC 300 globular cluster system using the Boller & Chivens (B&C) Spectrograph on the Baade Telescope in Chile. We confirm 9 probable globular clusters in NGC 300 and 3 possible clusters with very low radial velocities. For our full NGC 300 cluster sample, plus one cluster from the literature, we find a mean [Fe/H] = --0.94 +/- 0.15; without the 3 "possible" clusters we find a mean [Fe/H] = --0.98 +/- 0.12. We identify over 200 globular cluster candidates in HST I-band imaging, and spectroscopically confirm 62 new globular clusters in M81. The M81 globular cluster system shows marginal evidence for a bimodal metallicity distribution. The mean metallicity of 107 confirmed M81 globular clusters is [Fe/H] = 1.06 +/- 0.07. The M81 globular cluster system shows significant rotation, at 108 +/- 22 km s-1. There is evidence for a metallicity gradient among the metal-poor clusters. We perform HST ACS BV I photometry and radial profile fitting on 85 spectroscopically confirmed globular clusters, 136 "good" globular cluster candidates, and 198 other star cluster candidates. The globular cluster luminosity function peaks at V0 ˜20.26. The properties of the M81 globular cluster system are very similar to those of the Milky Way and M31, suggesting a similar origin for all three galaxies. Our understanding of the origins of spiral galaxy globular cluster systems would be vastly improved by comprehensive studies of low-mass and late-type spiral galaxies, including HST I-band imaging to identify globular cluster candidates for spectroscopic confirmation.

  12. The WAGGS project - I. The WiFeS Atlas of Galactic Globular cluster Spectra

    NASA Astrophysics Data System (ADS)

    Usher, Christopher; Pastorello, Nicola; Bellstedt, Sabine; Alabi, Adebusola; Cerulo, Pierluigi; Chevalier, Leonie; Fraser-McKelvie, Amelia; Penny, Samantha; Foster, Caroline; McDermid, Richard M.; Schiavon, Ricardo P.; Villaume, Alexa

    2017-07-01

    We present the WiFeS Atlas of Galactic Globular cluster Spectra, a library of integrated spectra of Milky Way and Local Group globular clusters. We used the WiFeS integral field spectrograph on the Australian National University 2.3 m telescope to observe the central regions of 64 Milky Way globular clusters and 22 globular clusters hosted by the Milky Way's low-mass satellite galaxies. The spectra have wider wavelength coverage (3300-9050 Å) and higher spectral resolution (R = 6800) than existing spectral libraries of Milky Way globular clusters. By including Large and Small Magellanic Cloud star clusters, we extend the coverage of parameter space of existing libraries towards young and intermediate ages. While testing stellar population synthesis models and analysis techniques is the main aim of this library, the observations may also further our understanding of the stellar populations of Local Group globular clusters and make possible the direct comparison of extragalactic globular cluster integrated light observations with well-understood globular clusters in the Milky Way. The integrated spectra are publicly available via the project website.

  13. 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.

  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. 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.

  16. 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.

  17. Insights into Hox Protein Function from a Large Scale Combinatorial Analysis of Protein Domains

    PubMed Central

    Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K.; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

    2011-01-01

    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. PMID:22046139

  18. 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.

  19. 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

  20. 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.

  1. Multiple Stellar Populations in Galactic Globular Clusters: General Properties

    NASA Astrophysics Data System (ADS)

    Piotto, Giampaolo

    2015-08-01

    Globular clusters are the most ancient stellar systems for which we can have a reliable age estimate, and therefore bring information on star formation processes in the early Universe. The discovery that these objects host different, distinct populations of stars drastically changed our view on their origin and evolution. Some of the most plausible scenarios able to account for the photometric and chemical properties of multiple stellar populations in globular clusters necessarily imply that these objects must have been much more massive in the past. Whether globular clusters should be considered either as remnants of massive star clusters or nuclei of former dwarf galaxies (or both of them) is an open issue. Surely, we need to better know the chemical and kinematical properties of the different populations hosted by single clusters, and their relation with the cluster parameters, in order to shed light on this problem. Determination of the basic properties of stars hosted by (young ) massive clusters, nuclear clusters, and dwarf galaxies and a comparison with the parameters characterizing multiple stellar populations in globular cluster is a complementary approach that shall be pursued.For the first time, in my talk, I will discuss the results of a large, legacy multi-wavelength, astrometric and photometric survey based on ACS and WFC3/HST observations which include UV data. A census of the presence and frequency of multiple populations in almost half of the globular clusters of our Galaxy, their chemical tagging, radial distribution and kinematics will be presented. The relation between multiple population properties and cluster parameters will be illustrated. Consequences of these observational facts on different scenarios proposed for the formation and evolution of globular cluster stars will be critically discussed. Future perspectives towards our understanding if this complex phenomenon will be highlighted.

  2. 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

  3. Shape-Dependent Global Deformation Modes of Large Protein Structures

    PubMed Central

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

    2010-01-01

    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 LeuTAa proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuTAa 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. PMID:20526444

  4. 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.

  5. 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.

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

    PubMed Central

    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 (≈89%) of the original associations. PMID:14566057

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Supra-galactic colour patterns in globular cluster systems

    NASA Astrophysics Data System (ADS)

    Forte, Juan C.

    2017-07-01

    An analysis of globular cluster systems associated with galaxies included in the Virgo and Fornax Hubble Space Telescope-Advanced Camera Surveys reveals distinct (g - z) colour modulation patterns. These features appear on composite samples of globular clusters and, most evidently, in galaxies with absolute magnitudes Mg in the range from -20.2 to -19.2. These colour modulations are also detectable on some samples of globular clusters in the central galaxies NGC 1399 and NGC 4486 (and confirmed on data sets obtained with different instruments and photometric systems), as well as in other bright galaxies in these clusters. After discarding field contamination, photometric errors and statistical effects, we conclude that these supra-galactic colour patterns are real and reflect some previously unknown characteristic. These features suggest that the globular cluster formation process was not entirely stochastic but included a fraction of clusters that formed in a rather synchronized fashion over large spatial scales, and in a tentative time lapse of about 1.5 Gy at redshifts z between 2 and 4. We speculate that the putative mechanism leading to that synchronism may be associated with large scale feedback effects connected with violent star-forming events and/or with supermassive black holes.

  12. 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

  13. 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.

  14. Complex protein nanopatterns over large areas via colloidal lithography.

    PubMed

    Kristensen, Stine H; Pedersen, Gitte A; Ogaki, Ryosuke; Bochenkov, Vladimir; Nejsum, Lene N; Sutherland, Duncan S

    2013-04-01

    The patterning of biomolecules at the nanoscale provides a powerful method to investigate cellular adhesion processes. A novel method for patterning is presented that is based on colloidal monolayer templating combined with multiple and angled deposition steps. Patterns of gold and SiO2 layers are used to generate complex protein nanopatterns over large areas. Simple circular patches or more complex ring structures are produced in addition to hierarchical patterns of smaller patches. The gold regions are modified through alkanethiol chemistry, which enables the preparation of extracellular matrix proteins (vitronectin) or cellular ligands (the extracellular domain of E-cadherin) in the nanopatterns, whereas the selective poly(l-lysine)-poly(ethylene glycol) functionalization of the SiO2 matrix renders it protein repellent. Cell studies, as a proof of principle, demonstrate the potential for using sets of systematically varied samples with simpler or more complex patterns for studies of cellular adhesive behavior and reveal that the local distribution of proteins within a simple patch critically influences cell adhesion. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  15. 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.

  16. 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

  17. 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.

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

    PubMed Central

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

    2015-01-01

    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. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations. PMID:25849493

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. Featured Image: Globular Cluster Orbits

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2017-04-01

    This figure (click for the full view) shows the meridional galactic orbits of 12 globular clusters that orbit the Milky Way. The recent release of stellar parallax data from Gaia allowed a team of scientists at Dartmouth College to improve measurements of a number of galactic globular clusters very old clusters of stars that can either orbit within the galactic disk and bulge or more distantly in the galactic halo. In a recent publication led by Erin OMalley, the team presents their findings and combines their new measurements for the clusters with proper motions from past studies to calculate the orbits that these globulars take. These calculations show us whether the clusters reside in the galactic disk and bulge (as only NGC 104 does in the sample shown here, since its orbit is confined to 8 kpc radially and 4 kpc vertically of the galactic center), or if they are halo clusters. To learn more about the authors work, you can check out the paper below!CitationErin M. OMalley et al 2017 ApJ 838 162. doi:10.3847/1538-4357/aa6574

  6. 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

  7. 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.

  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. 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.

  10. 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.

  11. ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction.

    PubMed

    Dhar, Jesmita; Chakrabarti, Pinak; Saini, Harpreet; Raghava, Gajendra Pal Singh; Kishore, Raghuvansh

    2015-02-01

    Mimicry of structural motifs is a common feature in proteins. The 10-membered hydrogen-bonded ring involving the main-chain C − O in a β-turn can be formed using a side-chain carbonyl group leading to Asx-turn. We show that the N − H component of hydrogen bond can be replaced by a C(γ) -H group in the side chain, culminating in a nonconventional C − H···O interaction. Because of its shape this β-turn mimic is designated as ω-turn, which is found to occur ∼ three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C − H···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ'1(i + 2) (using the interacting C(γ) atom). Based on these angles there are two types of ω-turns, each of which can be further divided into two groups. C(β) -branched side-chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal-binding sites. N-linked glycosylation occurs at the consensus pattern Asn-Xaa-Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω-turn, which may be the recognition site for protein modification. Location between two β-strands is the most common occurrence in protein tertiary structure, and being generally exposed ω-turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. © 2014 Wiley Periodicals, Inc.

  12. 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.

  13. A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

    PubMed Central

    Araya, Carlos L.; Fowler, Douglas M.; Chen, Wentao; Muniez, Ike; Kelly, Jeffery W.; Fields, Stanley

    2012-01-01

    The ability of a protein to carry out a given function results from fundamental physicochemical properties that include the protein’s structure, mechanism of action, and thermodynamic stability. Traditional approaches to study these properties have typically required the direct measurement of the property of interest, oftentimes a laborious undertaking. Although protein properties can be probed by mutagenesis, this approach has been limited by its low throughput. Recent technological developments have enabled the rapid quantification of a protein’s function, such as binding to a ligand, for numerous variants of that protein. Here, we measure the ability of 47,000 variants of a WW domain to bind to a peptide ligand and use these functional measurements to identify stabilizing mutations without directly assaying stability. Our approach is rooted in the well-established concept that protein function is closely related to stability. Protein function is generally reduced by destabilizing mutations, but this decrease can be rescued by stabilizing mutations. Based on this observation, we introduce partner potentiation, a metric that uses this rescue ability to identify stabilizing mutations, and identify 15 candidate stabilizing mutations in the WW domain. We tested six candidates by thermal denaturation and found two highly stabilizing mutations, one more stabilizing than any previously known mutation. Thus, physicochemical properties such as stability are latent within these large-scale protein functional data and can be revealed by systematic analysis. This approach should allow other protein properties to be discovered. PMID:23035249

  14. Binaries in Globular Clusters Multiple Populations

    NASA Astrophysics Data System (ADS)

    Lucatello, Sara; Sollima, Antonio; Gratton, Raffaele; D'Orazi, Valentina; Vesperini, Enrico; Carretta, Eugenio; Bragaglia, Angela

    2015-08-01

    In spite of considerable theoretical and obsservational effort, the series of events that leads to the formation of Globular Clusters and their multiple populations is still unclear.One of the key matters is where the so-called second generation of stars form and its distribution at the time of its birth with respect to the first generation. Some of the latest modeling has suggested that second generation should form in a compact subsystem concentrated in the inner regions of the primordial, first generation cluster. In this scenario, loss of a large fraction of the cluster mass is expected, mostly comprised of first generation stars. This would account for the mass budget issue (one of the main problems in the self-enrichment scenario) and would imply a considerable contribution of the clusters to the formation of the Galactic Halo.Testing this prediction is hence of great importance, but not so immediate. Long-term, dynamical evolution of multiple-population clusters could blur considerably the signature of the initial different concentrations, leaving at present time some memory in the very central part (Vesperini et al. 2013), which, because of its high density, is generally not accessible to the multi-object high resolution spectrographs that yield the spectra that allow the chemical composition measurements necessary to tag the different populations.An alternative approach to test the prediction of the initial segregation of the second generations is that of determining their binary fractions. In fact, until the two populations are completely mixed, second generation stars will evolve in a denser environment where disruption will occur more rapidly, leading to a smaller binary incidence in such population (Vesperini et al 2011).I will present the results of our long-term radial velocity monitoring of 10 Galactic Globular clusters, discuss the derived binary fractions in the two populations and address the implications of our findings on our understanding of

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. Supergiant molecular clouds and the formation of globular cluster systems

    NASA Astrophysics Data System (ADS)

    Harris, William E.; Pudritz, Ralph E.

    1994-07-01

    Data from several large elliptical and disk galaxies now show that globular clusters more massive than approximately 105 solar mass follow a power-law number distribution by mass, N approximately M-1.7, which is virtually independent of environment. Within observational uncertainty, this relation is identical to the shape of the mass distributions of giant molecular clouds (GMCs) in large spiral galaxies, the cloud cores embedded in GMCs, and giant H II regions in large spiral galaxies. We interpret this within a model whereby globular clusters formed out of dense cores within supergiant molecular clouds (SGMCs) that were present in the early protogalactic epoch. We construct a theory of pressure confined, self-gravitating, isothermal, magnetized molecular clouds and cores, based on the viral theorem and the observed mass spectra, and derive the characteristic physical properties of these parent SGMCs. These turn out to be of the right mass and density range to resemble the Searle-Zinn primordial fragments from which larger galaxies may have assembled. We suggest that the protocluster clouds were supported against gravitational collapse primarily by a combination of magnetic field pressure and Alfvenic turbulence, as is observed to be the case for contemporary molecular clouds. This approach removes the need for arbitrary external heat sources (such as long-lasting AGNs or Population III stars) to keep the clouds stable for long enough times to build up to globular-sized masses and more easily permits the global properties of the emergent clusters to be similar from one galaxy to another. By calculating lifetimes through a standard cloud growth model, we estimate that the principal epoch of globular cluster formation should have begun no earlier than a redshift of z approximately equal to 6.

  7. Large-scale proteomic analysis of membrane proteins

    SciTech Connect

    Ahram, Mamoun; Springer, David L.

    2004-10-01

    Proteomic analysis of membrane proteins is promising in identification of novel candidates as drug targets and/or disease biomarkers. Despite notable technological developments, obstacles related to extraction and solubilization of membrane proteins are frequently encountered. A critical discussion of the different preparative methods of membrane proteins is offered in relation to downstream proteomic applications, mainly gel-based analyses and mass spectrometry. Unknown proteins are often identified by high-throughput profiling of membrane proteins. In search for novel membrane proteins, analysis of protein sequences using computational tools is performed to predict for the presence of transmembrane domains. Here, we also present these bioinformatic tools with the human proteome as a case study. Along with technological innovations, advancements in the areas of sample preparation and computational prediction of membrane proteins will lead to exciting discoveries.

  8. Large-scale crystallization of proteins for purification and formulation.

    PubMed

    Hekmat, Dariusch

    2015-07-01

    Since about 170 years, salts were used to create supersaturated solutions and crystallize proteins. The dehydrating effect of salts as well as their kosmotropic or chaotropic character was revealed. Even the suitability of organic solvents for crystallization was already recognized. Interestingly, what was performed during the early times is still practiced today. A lot of effort was put into understanding the underlying physico-chemical interaction mechanisms leading to protein crystallization. However, it was understood that already the solvation of proteins is a highly complex process not to mention the intricate interrelation of electrostatic and hydrophobic interactions taking place. Although many basic questions are still unanswered, preparative protein crystallization was attempted as illustrated in the presented case studies. Due to the highly variable nature of crystallization, individual design of the crystallization process is needed in every single case. It was shown that preparative crystallization from impure protein solutions as a capture step is possible after applying adequate pre-treatment procedures like precipitation or extraction. Protein crystallization can replace one or more chromatography steps. It was further shown that crystallization can serve as an attractive alternative means for formulation of therapeutic proteins. Crystalline proteins can offer enhanced purity and enable highly concentrated doses of the active ingredient. Easy scalability of the proposed protein crystallization processes was shown using the maximum local energy dissipation as a suitable scale-up criterion. Molecular modeling and target-oriented protein engineering may allow protein crystallization to become part of a platform purification process in the near future.

  9. 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.

  10. Dynamical evolution of globular clusters: Recent developments

    NASA Astrophysics Data System (ADS)

    Merafina, Marco

    We analyze structural parameters of the globular clusters belonging to the Milky Way system which were listed in the latest edition of the Harris Catalogue. We search for observational evidences of the effect of tidal forces induced by the Galaxy on the dynamical and thermodynamical evolution of a globular cluster. The behavior for the W0 distribution exhibited by the globular cluster population seems to be in contrast with theoretical results in literature about gravothermal instability, and suggest a new limit value smaller than the previous one.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Stellar astrophysics: The mystery of globular clusters

    NASA Astrophysics Data System (ADS)

    Nota, Antonella; Charbonnel, Corinne

    2016-01-01

    The discovery of multiple stellar populations -- formed at different times -- in several young star clusters adds to the debate on the nature and origin of such populations in globular clusters from the early Universe. See Letter p.502

  1. The ACS Survey of Galactic Globular Clusters. VII. Relative Ages

    NASA Astrophysics Data System (ADS)

    Marín-Franch, Antonio; Aparicio, Antonio; Piotto, Giampaolo; Rosenberg, Alfred; Chaboyer, Brian; Sarajedini, Ata; Siegel, Michael; Anderson, Jay; Bedin, Luigi R.; Dotter, Aaron; Hempel, Maren; King, Ivan; Majewski, Steven; Milone, Antonino P.; Paust, Nathaniel; Reid, I. Neill

    2009-04-01

    The ACS Survey of Galactic globular clusters is a Hubble Space Telescope Treasury program designed to provide a new large, deep, and homogeneous photometric database. Based on observations from this program, we have measured precise relative ages for a sample of 64 Galactic globular clusters by comparing the relative position of the clusters' main-sequence (MS) turnoffs, using MS fitting to cross-compare clusters within the sample. This method provides relative ages to a formal precision of 2%-7%. We demonstrate that the calculated relative ages are independent of the choice of theoretical model. We find that the Galactic globular cluster sample can be divided into two groups—a population of old clusters with an age dispersion of ~5% and no age-metallicity relation, and a group of younger clusters with an age-metallicity relation similar to that of the globular clusters associated with the Sagittarius dwarf galaxy. These results are consistent with the Milky Way halo having formed in two phases or processes. The first one would be compatible with a rapid (<0.8 Gyr) assembling process of the halo, in which the clusters in the old group were formed. Also these clusters could have been formed before re-ionization in dwarf galaxies that would later merge to build the Milky Way halo as predicted by ΛCDM cosmology. However, the galactocentric metallicity gradient shown by these clusters seems difficult to reconcile with the latter. As for the younger clusters, it is very tempting to argue that their origin is related to their formation within Milky Way satellite galaxies that were later accreted, but the origin of the age-metallicity relation remains unclear. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555, under program GO-10775 (PI: A. Sarajedini).

  2. The PDZ protein discs-large (DLG): the 'Jekyll and Hyde' of the epithelial polarity proteins.

    PubMed

    Roberts, Sally; Delury, Craig; Marsh, Elizabeth

    2012-10-01

    Discs-large (DLG) is a multi-PDZ domain-containing protein that belongs to the family of molecular scaffolding proteins known as membrane guanylate kinases or MAGUKs. DLG is a component of the Scribble polarity complex and genetic analyses of DLG in Drosophila have identified a role for the protein in several key biological processes including the regulation of apico-basal polarity of epithelial cells, as well as other polarity processes such as asymmetric cell division and cell invasion. Disturbance of DLG function leads to uncontrolled epithelial cell proliferation and neoplastic transformation, thereby defining DLG as a potential tumour suppressor. However, whether mammalian homologues of DLG (DLG1, DLG2, DLG3 and DLG4) also possess tumour suppressor functions is not known. In this minireview, we focus on the biological functions of DLG1 in human epithelial cells and on how the function of this MAGUK relates to its intracellular location. We examine some of the evidence that implies that DLG has both tumour suppressor and, paradoxically, oncogenic functions depending upon the precise cellular context. © 2012 The Authors Journal compilation © 2012 FEBS.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Evidence for an Accretion Origin for the Outer Halo Globular Cluster System of M31

    NASA Astrophysics Data System (ADS)

    Mackey, A. D.; Huxor, A. P.; Ferguson, A. M. N.; Irwin, M. J.; Tanvir, N. R.; McConnachie, A. W.; Ibata, R. A.; Chapman, S. C.; 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 ≈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. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii.

  9. 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.

  10. Large scale purification of rapeseed proteins (Brassica napus L.).

    PubMed

    Bérot, S; Compoint, J P; Larré, C; Malabat, C; Guéguen, J

    2005-04-15

    Rapeseed (Brassica napus L.) cruciferin (12S globulin), napin (2S albumin) and lipid transfer proteins (LTP) were purified at a multi-g scale. The procedure developed was simple, rather fast and resolutive; it permitted the recovery of these proteins with a good yield, such as 40% for cruciferin and 18% for napin. Nanofiltration eliminated the major phenolic compounds. The remaining protein fraction was fractionated by cation exchange chromatography (CEC) on a streamline SP-XL column in alkaline conditions. The unbound neutral cruciferin was polished by size exclusion chromatography. The alkaline napin isoforms and LTP, adsorbed on the beads, were eluted as a whole fraction and further separated by an other CEC step at acidic pH. Napins were polished by hydrophobic interaction chromatography (HIC). The fractions were characterized by reverse phase HPLC, electrophoresis, N-terminal sequencing and mass spectrometry. All the fractions contained less than 5% of impurities.

  11. Hot Subdwarfs in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Moehler, S.; Heber, U.; Saffer, R.; Thejll, P.

    1995-12-01

    We will present data on sdB stars in the globular clusters M 15, M 22, and NGC 6752. While NGC 6752 has been known to harbour sdBs for quite some time already (Heber et al., 1986), it has also been the only globular cluster known to do so. Only recently, sdB candidates in M 15 (Durrell & Harris, 1993) and in M 22 (Thejll, priv. comm) have been discovered. An analysis of one of the sdBs in M 15 was presented recently (Moehler, in press), while the data on the ones in M 22 will be shown at this meeting for the first time. The physical parameters of these stars (teff and log g ) are derived from optical and IUE spectrophotometric data, intermediate resolution spectroscopy and Stromgren photometry. Knowing the distances of the clusters we can also determine masses. We want to compare the physical parameters of these stars for the different clusters to see what their evolutionary status is and how (or whether at all) it is affected by metallicity. We will also compare our findings to sdB stars found in the field of the Milky Way. In addition we want to see whether the problems encountered with the analyses of blue HB stars (Moehler et al., 1995) apply also to the sdB stars. These analyses showed the BHB stars to have significantly lower surface gravities and masses than predicted by theory. It turned out that this effect did not extend to the sdBs in NGC 6752 studied by Heber et al. (1986) which however constituted a sample too small to draw any meaningful conclusions. Durrell P.R., Harris W.E., 1993, AJ{105}{1420} Heber U., Kudritzki R.P., Caloi V., Castellani V., Danziger J., Gilmozzi R., 1986, \\aua{162}{171--179} Moehler S., Heber U., de Boer K.S., 1995, \\aua{294}{65} Moehler S., 1995, to appear in The Formation of the Galactic Halo - Inside and Out}, Proceedings of the meeting at Tucson, Oct. 9-11, 1995, ASP Conf. Ser.

  12. Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists.

    PubMed

    Koes, David; Khoury, Kareem; Huang, Yijun; Wang, Wei; Bista, Michal; Popowicz, Grzegorz M; Wolf, Siglinde; Holak, Tad A; Dömling, Alexander; Camacho, Carlos J

    2012-01-01

    Although there is no shortage of potential drug targets, there are only a handful known low-molecular-weight inhibitors of protein-protein interactions (PPIs). One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, we developed a novel pharmacophore-based interactive screening technology that builds on the role anchor residues, or deeply buried hot spots, have in PPIs, and redesigns these entry points with anchor-biased virtual multicomponent reactions, delivering tens of millions of readily synthesizable novel compounds. Application of this approach to the MDM2/p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors, and co-crystal structures validate the designed compounds. Our unique open-access technology promises to expand chemical space and the exploration of the human interactome by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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…

  18. 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…

  19. Mass evaporation rate of globular clusters in a strong tidal field

    NASA Astrophysics Data System (ADS)

    Madrid, Juan P.; Leigh, Nathan W. C.; Hurley, Jarrod R.; Giersz, Mirek

    2017-09-01

    The mass evaporation rate of globular clusters evolving in a strong Galactic tidal field is derived through the analysis of large, multimass N-body simulations. For comparison, we also study the same evaporation rates using mocca Monte Carlo models for globular cluster evolution. Our results show that the mass evaporation rate is a dynamical value, that is, far from a constant single number found in earlier analytical work and commonly used in the literature. Moreover, the evaporation rate derived with these simulations is higher than values previously published. These models also show that the value of the mass evaporation rate depends on the strength of the tidal field. We give an analytical estimate of the mass evaporation rate as a function of time and galactocentric distance ξ(RGC, t). Upon extrapolating this formula to smaller RGC values, our results provide tentative evidence for a very high ξ value at small RGC. Our results suggest that the corresponding mass-loss in the inner Galactic potential could be high and it should be accounted for when star clusters pass within it. This has direct relevance to nuclear cluster formation/growth via the infall of globular clusters through dynamical friction. As an illustrative example, we estimate how the evaporation rate increases for an ∼105 M⊙ globular cluster that decays through dynamical friction into the Galactic Centre. We discuss the findings of this work in relation to the formation of nuclear star clusters by inspiralling globular clusters.

  20. 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.

  1. Variable stars in the VVV globular clusters

    NASA Astrophysics Data System (ADS)

    Alonso-García, Javier; Catelan, Márcio; Ramos, Rodrigo Contreras; Dékány, István; Minniti, Dante

    2017-09-01

    The VVV survey observed some of the most crowded and most obscured regions in the inner MilkyWay during the last years. A significant sample of the less known globular clusters in our galaxy lie there. Combining the high-resolution, wide-field, nearinfrared capabilities of the survey camera, the use of 5 different filters, and multi-epoch observations, we are able to overcome many of the previous challenges that prevented a proper study of these objects. Particularly, the identification of the RR Lyrae stars in these globular clusters is proving to be a fundamental tool to establish accurately their distances and reddenings, and to infer information about the Oosterhoff dichotomy that Galactic globular clusters seem to follow.

  2. 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.

  3. Globular Cluster Messier 2 in Aquarius

    NASA Image and Video Library

    2003-12-11

    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. http://photojournal.jpl.nasa.gov/catalog/PIA04926

  4. 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.

  5. 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.

  6. 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.

  7. The Structural Parameters of the Globular Clusters in M31 with PAndAS

    NASA Astrophysics Data System (ADS)

    Woodley, Kristin; Pan-Andromeda Archaeological Survey (PAndAS), The

    2012-05-01

    The Pan-Andromeda Archaeological Survey (PAndAS) has obtained images with the Canada France Hawaii Telescope using the instrument MegaCam, covering over 400 square degrees in the sky and extending beyond 150 kpc in radius from the center of M31. With this extensive data set, we have measured the structural parameters of all confirmed globular clusters in M31 as well as for a large fraction of the candidate globular clusters in the Revised Bologna Catalog V.4 (Galleti et al. 2004, A&A, 416, 917). In this paper, we present their parameters, including their core-, effective (half-light)-, and tidal radii, as well as their ellipticities measured in a homogeneous manner with ISHAPE (Larsen 1999, A&AS, 139, 393). We examine these parameters as functions of radial position, luminosity, color, metallicity, and age. We also use our measurements as an additional parameter to help constrain the candidacy of the unconfirmed globular clusters.

  8. Collisions of Free-floating Planets with Evolved Stars in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Soker, Noam; Rappaport, Saul; Fregeau, John

    2001-12-01

    We estimate the rate of collisions between stars and free-floating planets (FFPs) in globular clusters, in particular, the collision of FFPs with red giant branch (RGB) stars. Recent dynamical simulations imply that the density of such objects could exceed ~106 pc-3 near the cores of rich globular clusters. We show that in these clusters ~5%-10% of all RGB stars near the core would suffer a collision with an FFP and that such a collision can spin up the RGB star's envelope by an order of magnitude. In turn, the higher rotation rates may lead to enhanced mass-loss rates on the RGB, which could result in bluer horizontal branch (HB) stars. Hence, it is plausible that the presence of a large population of FFPs in a globular cluster can influence the distribution of stars on the HB of that cluster to a detectable degree.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Large scale analysis of protein stability in OMIM disease related human protein variants.

    PubMed

    Martelli, Pier Luigi; Fariselli, Piero; Savojardo, Castrense; Babbi, Giulia; Aggazio, Francesco; Casadio, Rita

    2016-06-23

    Modern genomic techniques allow to associate several Mendelian human diseases to single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears to assume a particular relevance in annotating whether a single residue substitution can or cannot be associated to a given disease. Thermodynamic properties of human proteins and of their disease related variants are lacking. In the present work, we take advantage of the available three dimensional structure of human proteins for predicting the role of disease related variations on the perturbation of protein stability. We develop INPS3D, a new predictor based on protein structure for computing the effect of single residue variations on protein stability (ΔΔG), scoring at the state-of-the-art (Pearson's correlation value of the regression is equal to 0.72 with mean standard error of 1.15 kcal/mol on a blind test set comprising 351 variations in 60 proteins). We then filter 368 OMIM disease related proteins known with atomic resolution (where the three dimensional structure covers at least 70 % of the sequence) with 4717 disease related single residue variations and 685 polymorphisms without clinical consequence. We find that the effect on protein stability of disease related variations is larger than the effect of polymorphisms: in particular, by setting to |1 kcal/mol| the threshold between perturbing and not perturbing variations of the protein stability, about 44 % of disease related variations and 20 % of polymorphisms are predicted with |ΔΔG| > 1 kcal/mol, respectively. A consistent fraction of OMIM disease related variations is however predicted to promote |ΔΔG| ≤ 1 kcal/mol and we focus here on detecting features that can be associated to the thermodynamic property of the protein variant. Our analysis reveals that some 47 % of disease related variations

  14. 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

  15. 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

  16. 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

  17. 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.

  18. Globular cluster systems as clues to galaxy evolution

    NASA Technical Reports Server (NTRS)

    Zepf, Stephen E.; Ashman, Keith M.

    1993-01-01

    We investigate the properties of systems of globular clusters in light of the hypothesis that galaxy mergers play a major role in galaxy evolution. In a previous paper, we presented a model in which the formation of globular clusters occurs during galaxy interactions and mergers. We discussed several predictions of the model, including the existence of young globular clusters in currently merging galaxies and the presence of two or more metallicity peaks in the globular clusters systems of normal elliptical galaxies. Here, we present recent observational evidence which supports both of these predictions and suggests that mergers may have a significant influence on the formation and evolution of galaxies and their globular clusters.

  19. 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.

  20. 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.

  1. 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.

  2. Characterization of Protein-Protein Interfaces in Large Complexes by Solid-State NMR Solvent Paramagnetic Relaxation Enhancements.

    PubMed

    Öster, Carl; Kosol, Simone; Hartlmüller, Christoph; Lamley, Jonathan M; Iuga, Dinu; Oss, Andres; Org, Mai-Liis; Vanatalu, Kalju; Samoson, Ago; Madl, Tobias; Lewandowski, Józef R

    2017-09-06

    Solid-state NMR is becoming a viable alternative for obtaining information about structures and dynamics of large biomolecular complexes, including ones that are not accessible to other high-resolution biophysical techniques. In this context, methods for probing protein-protein interfaces at atomic resolution are highly desirable. Solvent paramagnetic relaxation enhancements (sPREs) proved to be a powerful method for probing protein-protein interfaces in large complexes in solution but have not been employed toward this goal in the solid state. We demonstrate that (1)H and (15)N relaxation-based sPREs provide a powerful tool for characterizing intermolecular interactions in large assemblies in the solid state. We present approaches for measuring sPREs in practically the entire range of magic angle spinning frequencies used for biomolecular studies and discuss their benefits and limitations. We validate the approach on crystalline GB1, with our experimental results in good agreement with theoretical predictions. Finally, we use sPREs to characterize protein-protein interfaces in the GB1 complex with immunoglobulin G (IgG). Our results suggest the potential existence of an additional binding site and provide new insights into GB1:IgG complex structure that amend and revise the current model available from studies with IgG fragments. We demonstrate sPREs as a practical, widely applicable, robust, and very sensitive technique for determining intermolecular interaction interfaces in large biomolecular complexes in the solid state.

  3. Large-Scale Protein-Protein Interaction Analysis in Arabidopsis Mesophyll Protoplasts by Split Firefly Luciferase Complementation

    PubMed Central

    Li, Jian-Feng; Bush, Jenifer; Xiong, Yan; Li, Lei; McCormack, Matthew

    2011-01-01

    Protein-protein interactions (PPIs) constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC) as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs) and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens. PMID:22096563

  4. 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.

  5. RR Lyrae Variables in Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Catelan, M.; Contreras, R.; Salinas, R.; Escobar, M. E.; Smith, H. A.; De Lee, N.; Pritzl, B. J.; Borissova, J.

    2004-12-01

    RR Lyrae variables are the cornerstone of the Population II distance scale, and yet our knowledge of the RR Lyrae variable star content in Galactic globular clusters is now known to be surprisingly incomplete. In the present paper, we present our new results in this area. Highlights of our work includes: i) The discovery of a vast number of variable stars in M62 (NGC 6266), making it one of the three most RR Lyrae-rich globular clusters known, and also placing it as Oosterhoff type I in spite of a blue horizontal branch morphology; ii) The determination of light curves and Oosterhoff types for globular clusters associated with the Sagittarius dSph galaxy, including NGC 5634, Arp 2, and Terzan 8; iii) A reassessment of the variable star content in the moderately metal-rich globular clusters M69 and NGC 6304; iv) The first theoretical calibration of the RR Lyrae period-luminosity-metallicity relation in I, J, and H, as well as an updated calibration of the K-band relation---along with comparisons against the empirical data, particularly in I. This project was supported in part by Proyecto Fondecyt Regular 1030954.

  6. 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.

  7. 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.

  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. 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.

  10. Globular cluster x-ray sources

    PubMed Central

    Pooley, David

    2010-01-01

    Globular clusters and x-ray astronomy have a long and fruitful history. Uhuru and OSO-7 revealed highly luminous (> 1036 ergs-1) x-ray sources in globular clusters, and Einstein and ROSAT revealed a larger population of low-luminosity (< 1033 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. PMID:20404204

  11. 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.

  12. 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.

  13. fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data

    PubMed Central

    Hung, Ling-Hong; Samudrala, Ram

    2014-01-01

    Motivation: fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project. Results: fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco. Availability and implementation: fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster) Contact: lhhung@compbio.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24532722

  14. fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.

    PubMed

    Hung, Ling-Hong; Samudrala, Ram

    2014-06-15

    fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project. fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco. fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster) © The Author 2014. Published by Oxford University Press.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. The outer halo globular cluster system of M31 - II. Kinematics

    NASA Astrophysics Data System (ADS)

    Veljanoski, J.; Mackey, A. D.; Ferguson, A. M. N.; Huxor, A. P.; Côté, P.; Irwin, M. J.; Tanvir, N. R.; Peñarrubia, J.; Bernard, E. J.; Fardal, M.; Martin, N. F.; McConnachie, A.; Lewis, G. F.; Chapman, S. C.; Ibata, R. A.; Babul, A.

    2014-08-01

    We present a detailed kinematic analysis of the outer halo globular cluster system of the Andromeda galaxy (M31). Our basis for this is a set of new spectroscopic observations for 78 clusters lying at projected distances between Rproj ˜ 20-140 kpc from the M31 centre. These are largely drawn from the recent Pan-Andromeda Archaeological Survey globular cluster catalogue; 63 of our targets have no previous velocity data. Via a Bayesian maximum likelihood analysis, we find that globular clusters with Rproj > 30 kpc exhibit coherent rotation around the minor optical axis of M31, in the same direction as more centrally located globular clusters, but with a smaller amplitude of 86 ± 17 km s-1. There is also evidence that the velocity dispersion of the outer halo globular cluster system decreases as a function of projected distance from the M31 centre, and that this relation can be well described by a power law of index ≈ -0.5. The velocity dispersion profile of the outer halo globular clusters is quite similar to that of the halo stars, at least out to the radius up to which there is available information on the stellar kinematics. We detect and discuss various velocity correlations amongst subgroups of globular clusters that lie on stellar debris streams in the M31 halo. Many of these subgroups are dynamically cold, exhibiting internal velocity dispersions consistent with zero. Simple Monte Carlo experiments imply that such configurations are unlikely to form by chance, adding weight to the notion that a significant fraction of the outer halo globular clusters in M31 have been accreted alongside their parent dwarf galaxies. We also estimate the M31 mass within 200 kpc via the Tracer Mass Estimator (TME), finding (1.2-1.6) ± 0.2 × 1012 M⊙. This quantity is subject to additional systematic effects due to various limitations of the data, and assumptions built in into the TME. Finally, we discuss our results in the context of formation scenarios for the M31 halo.

  4. 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

  5. HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project.

    PubMed Central

    Suyama, M; Nagase, T; Ohara, O

    1999-01-01

    HUGE is a database for human large proteins newly identified by Kazusa cDNA project, which aims to predict protein primary structures from sequences of human large cDNAs (>4 kb). In particular, cDNA clones capable of coding for large proteins (>50 kDa) are current targets of the project. More than 700 sequences of human cDNAs (average size, 5.1 kb) have been determined to date and deposited in the public databases. Notable information implied from the cDNAs and the predicted protein sequences can be obtained through HUGE via the World Wide Web at URL http://www.kazusa.or.jp/huge PMID:9847221

  6. Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces.

    PubMed

    Inhester, Therese; Bietz, Stefan; Hilbig, Matthias; Schmidt, Robert; Rarey, Matthias

    2017-02-27

    Comparison of three-dimensional interaction patterns in large collections of protein-ligand interfaces is a key element for understanding protein-ligand interactions and supports various steps in the structure-based drug design process. Different methods exist that provide query systems to search for geometrical patterns in protein-ligand complexes. However, these tools do not meet all of the requirements, which are high query variability, an adjustable search set, and high retrieval speed. Here we present a new tool named PELIKAN that is able to search for a variety of geometrical queries in large protein structure collections in a reasonably short time. The data are stored in an SQLite database that can easily be constructed from any set of protein-ligand complexes. We present different test queries demonstrating the performance of the PELIKAN approach. Furthermore, two application scenarios show the usefulness of PELIKAN in structure-based design endeavors.

  7. Health Benefits of Texturized Whey Proteins

    USDA-ARS?s Scientific Manuscript database

    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. Aberrantly Large Single-Channel Conductance of Polyhistidine Arm-Containing Protein Nanopores.

    PubMed

    Thakur, Avinash Kumar; Larimi, Motahareh Ghahari; Gooden, Kristin; Movileanu, Liviu

    2017-09-12

    There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of the relatively short size of the tags, they are often thought to have little or no effect on the conformation or activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of a hexahistidine arm at the N-terminus of a truncated FhuA-based protein nanopore, leaving the C-terminus untagged, produces an unusual increase in the unitary conductance to ∼8 nS in 1 M KCl. To the best of our knowledge, this is the largest single-channel conductance ever recorded with a monomeric β-barrel outer membrane protein. The hexahistidine arm was captured by an anti-polyhistidine tag monoclonal antibody added to the side of the channel-forming protein addition, but not to the opposite side, documenting that this truncated FhuA-based protein nanopore inserts into a planar lipid bilayer with a preferred orientation. This finding is in agreement with the protein insertion in vivo, in which the large loops face the extracellular side of the membrane. The aberrantly large single-channel conductance, likely induced by a greater cross-sectional area of the pore lumen, along with the vectorial insertion into a lipid membrane, will have profound implications for further developments of engineered protein nanopores.

  9. 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.

  10. 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.

  11. 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.

  12. The self-enrichment of globular clusters

    SciTech Connect

    Morgan, S.; Lake, G.

    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 supernova detonation. If this is the case, the minimum mass of a globular cluster is about 10 to the 4.6th solar mass. 24 refs.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Modelling the Milky Way's globular cluster system

    NASA Astrophysics Data System (ADS)

    Binney, James; Wong, Leong Khim

    2017-05-01

    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.

  1. 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.

  2. Globular Cluster Systems along the Hubble Sequence

    NASA Astrophysics Data System (ADS)

    Huizinga, Edwin

    1996-07-01

    Globular Cluster Systems {GCSs} provide a powerful tool to differentiate between competing galaxy formation- and evolution scenarios. However, our current knowledge of GCS in spiral galaxies is based mainly on studies of the Galaxy and M31. Even though GCSs have been detected in other spiral galaxies, ground-based observations barely reach the peak of the Globular-Cluster luminosity function, and do not provide accurate colors. We propose a systematic study of the GCSs in 6 edge-on L* spiral galaxies beyond the Local Group, using WFPC2. These galaxies were carefully selected to meet several stringent criteria. With the new dithering techniques, it will be possible to resolve any faint background galaxies and obtain a clean sample of globular clusters for all galaxies in our sample. This will allow us to study the complete luminosity functions, {V-I} color distributions, and GCS richness for L* galaxies as a function of Hubble type {Sa, Sb, Sc}. These data will be used to study the relations between the galaxies' bulge and {thin/thick} disk properties and their GCSs. If, for example, GCS properties correlate with bulge properties, this will rule out any strong evolution along the Hubble Sequence towards earlier type spirals, from Sc to Sa, as has recently been proposed by Pfenniger et al. {1994}.

  3. 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.

  4. 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.

  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. 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

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

    PubMed Central

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

    2011-01-01

    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. PMID:21671455

  8. 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.

  9. Young accreted globular clusters in the outer halo of M31

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    We report on observations of two newly discovered globular clusters in the outskirts of M31 made using the Gemini Multi-Object Spectrograph (GMOS) instrument on Gemini North. These objects, PAndAS-7 (PA-7) and PAndAS-8 (PA-8), lie at a galactocentric radius of ≈87 kpc and are projected, with separation ≈19 kpc, on to a field halo substructure known as the South-West Cloud. We measure radial velocities for the two clusters which confirm that they are almost certainly physically associated with this feature. Colour-magnitude diagrams reveal strikingly short, exclusively red horizontal branches in both PA-7 and PA-8; both also have photometric [Fe/H] = -1.35 ± 0.15. At this metallicity, the morphology of the horizontal branch is maximally sensitive to age, and we use the distinctive configurations seen in PA-7 and PA-8 to demonstrate that both objects are very likely to be at least 2 Gyr younger than the oldest Milky Way globular clusters. Our observations provide strong evidence for young globular clusters being accreted into the remote outer regions of M31 in a manner entirely consistent with the established picture for the Milky Way, and add credence to the idea that similar processes play a central role in determining the composition of globular cluster systems in large spiral galaxies in general.

  10. 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.

  11. 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.

  12. 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.

  13. The Faint Globular Cluster in the Dwarf Galaxy Andromeda I

    NASA Astrophysics Data System (ADS)

    Caldwell, Nelson; Strader, Jay; Sand, David J.; Willman, Beth; Seth, Anil C.

    2017-09-01

    Observations of globular clusters in dwarf galaxies can be used to study a variety of topics, including the structure of dark matter halos and the history of vigorous star formation in low-mass galaxies. We report on the properties of the faint globular cluster (M V -3.4) in the M31 dwarf galaxy Andromeda I. This object adds to the growing population of low-luminosity Local Group galaxies that host single globular clusters.

  14. 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.

  15. Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein.

    PubMed

    Pirchi, Menahem; Ziv, Guy; Riven, Inbal; Cohen, Sharona Sedghani; Zohar, Nir; Barak, Yoav; Haran, Gilad

    2011-10-11

    Proteins attain their function only after folding into a highly organized three-dimensional structure. Much remains to be learned about the mechanisms of folding of large multidomain proteins, which may populate metastable intermediate states on their energy landscapes. Here we introduce a novel method, based on high-throughput single-molecule fluorescence experiments, which is specifically geared towards tracing the dynamics of folding in the presence of a plethora of intermediates. We employ this method to characterize the folding reaction of a three-domain protein, adenylate kinase. Using thousands of single-molecule trajectories and hidden Markov modelling, we identify six metastable states on adenylate kinase's folding landscape. Remarkably, the connectivity of the intermediates depends on denaturant concentration; at low concentration, multiple intersecting folding pathways co-exist. We anticipate that the methodology introduced here will find broad applicability in the study of folding of large proteins, and will provide a more realistic scenario of their conformational dynamics.

  16. Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide.

    PubMed

    Lee, Seonghyun; Jo, Kyubong

    2016-06-23

    Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).

  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. 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.

  19. 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.

  20. Gravitational interactions between globular and open clusters: an introduction

    NASA Astrophysics Data System (ADS)

    de la Fuente Marcos, R.; de la Fuente Marcos, C.; Reilly, D.

    2014-01-01

    Historically, it has been assumed that globular and open clusters never interact. However, recent evidence suggests that: globular clusters passing through the disk may be able to perturb giant molecular clouds (GMCs) triggering formation of open clusters and some old open clusters may be linked to accreted globulars. Here, we further explore the existence of possible dynamical connections between globular and open clusters, and realize that the most obvious link must be in the form of gravitational interactions. If open clusters are born out of GMCs, they have to move in similar orbits. If we accept that globulars can interact with GMCs, triggering star formation, it follows that globular and open clusters must also interact. Consistently, theoretical arguments as well as observational evidence, show that globular and open clusters certainly are interacting populations and their interactions are far more common than usually thought, especially for objects part of the bulge/disk. Monte Carlo calculations confirm that conclusion. Globular clusters seem capable of not only inducing formation of open clusters but, more often, their demise. Relatively frequent high speed cluster encounters or cluster harassment may also cause, on the long-term, slow erosion and tidal truncation on the globulars involved. The disputed object FSR 1767 (2MASS-GC04) may be, statistically speaking, the best example of an ongoing interaction.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Globular Cluster Star Classification: Application to M13

    NASA Astrophysics Data System (ADS)

    Caimmi, R.

    2013-06-01

    Starting from recent determination of Fe, O, Na abundances on a restricted sample (N=67) of halo and thick disk stars, a natural and well motivated selection criterion is defined for the classification globular cluster stars. An application is performed to M13 using a sample (N=113) for which Fe, O, Na abundances have been recently inferred from observations. A comparison is made between the current and earlier M13 star classifications. Both O and Na empirical differential abundance distributions are determined for each class and for the whole sample (with the addition of Fe in the last case) and compared with their theoretical counterparts due to cosmic scatter obeying a Gaussian distribution whose parameters are inferred from related subsamples. The occurrence of an agreement between the empirical and theoretical distributions is interpreted as absence of significant chemical evolution and vice versa. The procedure is repeated with regard to four additional classes depending on whether oxygen and sodium abundance is above (stage CE) or below (stage AF) a selected threshold. Both O and Na empirical differential abundance distributions, related to the whole sample, exhibit a linear fit for the AF and CE stage. Within the errors, the oxygen slope for the CE stage is equal and of opposite sign with respect to the sodium slope for AF stage, while the contrary holds when dealing with the oxygen slope for the AF stage with respect to the sodium slope for the CE stage. In the light of simple models of chemical evolution applied to M13, oxygen depletion appears to be mainly turned into sodium enrichment for [O/H]≥-1.35 and [Na/H]≤-1.45, while one or more largely preferred channels occur for [O/H]<-1.35 and [Na/H]>-1.45. In addition, the primordial to the current M13 mass ratio can be inferred from the true sodium yield in units of the sodium solar abundance. Though the above results are mainly qualitative due to large (∓.5 dex) uncertainties in abundance

  7. 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.

  8. XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.

    PubMed

    Schweppe, Devin K; Zheng, Chunxiang; Chavez, Juan D; Navare, Arti T; Wu, Xia; Eng, Jimmy K; Bruce, James E

    2016-09-01

    Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein-protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis. XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/ : jimbruce@uw.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Large-scale Epstein-Barr virus EBNA1 protein purification.

    PubMed

    Duellman, Sarah J; Burgess, Richard R

    2009-02-01

    The protein-DNA and protein-protein interactions of Epstein-Barr virus nuclear antigen 1 (EBNA1) are known to play an important role in the many functions of this viral protein. Large quantities of pure EBNA1 protein would be useful in biochemical assays to elucidate such interactions. In particular, the crystal structure of the full-length protein would be important to show possible regions of interaction and/or post-translational modification. Recently, we described a novel approach to overexpress and purify EBNA1 from Escherichia coli; however, it is not ideal for large-scale production of EBNA1. We were able to optimize this protocol by (1) adding a polyethyleneimine precipitation step prior to Ni-NTA chromatography to reduce complexity of the sample and remove nucleic acid, (2) optimizing the Ni-NTA gradient to further separate EBNA1 from impurities, and (3) concluding with a MonoS cation-exchange chromatography step to further purify and concentrate EBNA1. We were able to recover 10-mg quantities of pure EBNA1 protein.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

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

    PubMed Central

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

    2011-01-01

    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. PMID:21784873

  16. 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

  17. 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.

  18. 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)

  19. 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)

  20. 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

  1. Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations

    PubMed Central

    Dai, Liang; Zhou, Yaoqi

    2011-01-01

    Worldwide structural genomics projects are increasing structure coverage of sequence space but have not significantly expanded the protein structure space itself (i.e. number of unique structural folds) since 2007. Discovering new structural folds experimentally by directed evolution and random recombination of secondary-structure blocks is also proved rarely successful. Meanwhile, previous computational efforts for large-scale mapping of protein structure space are limited to simple model proteins and led to an inconclusive answer on the completeness of the existing, observed protein structure space. Here, we build novel protein structures by extending naturally occurring circular (single-loop) permutation to multiple-loop permutations (MLP). These structures are clustered by structural similarity measure called TM-Score. The computational technique allows us to produce different structural clusters on the same naturally occurring, packed, stable core but with alternatively connected secondary-structure segments. A large-scale MLP of 2936 SCOP domains reproduces those existing structural clusters (63%) mostly as hubs for many non-redundant sequences and illustrates newly discovered novel clusters as islands adopted by a few sequences only. Results further show that there exist a significant number of novel, potentially stable clusters for medium or large-size single-domain proteins, in particular (>100 amino-acid residues) that are either not yet adopted by nature or adopted only by a few sequences. This study suggests that MLP provides a simple yet highly effective tool for engineering and design of novel protein structures (including naturally knotted proteins). The implication of recovering CASP new-fold targets by MLP on template-based structure prediction is also discussed. Our MLP structures are available for download at the publication page of the website http://sparks.informatics.iupui.edu. PMID:21376059

  2. Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics.

    PubMed

    Kim, Jae In; Na, Sungsoo; Eom, Kilho

    2011-01-15

    Normal mode analysis (NMA) with coarse-grained model, such as elastic network model (ENM), has allowed the quantitative understanding of protein dynamics. As the protein size is increased, there emerges the expensive computational process to find the dynamically important low-frequency normal modes due to diagonalization of massive Hessian matrix. In this study, we have provided the domain decomposition-based structural condensation method that enables the efficient computations on low-frequency motions. Specifically, our coarse-graining method is established by coupling between model condensation (MC; Eom et al., J Comput Chem 2007, 28, 1400) and component mode synthesis (Kim et al., J Chem Theor Comput 2009, 5, 1931). A protein structure is first decomposed into substructural units, and then each substructural unit is coarse-grained by MC. Once the NMA is implemented to coarse-grained substructural units, normal modes and natural frequencies for each coarse-grained substructural unit are assembled by using geometric constraints to provide the normal modes and natural frequencies for whole protein structure. It is shown that our coarse-graining method enhances the computational efficiency for analysis of large protein complexes. It is clearly suggested that our coarse-graining method provides the B-factors of 100 large proteins, quantitatively comparable with those obtained from original NMA, with computational efficiency. Moreover, the collective behaviors and/or the correlated motions for model proteins are well delineated by our suggested coarse-grained models, quantitatively comparable with those computed from original NMA. It is implied that our coarse-grained method enables the computationally efficient studies on conformational dynamics of large protein complex.

  3. 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

  4. 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.

  5. The Globular Cluster Relative Ages and the Milky Way Formation Time Scale

    NASA Astrophysics Data System (ADS)

    Aparicio, Antonio; Marín-Franch, Antonio; Piotto, Giampaolo; Rosenberg, Alfred; Chaboyer, Brian; Sarajedini, Ata; Siegel, Michael; Anderson, Jay; Bedin, Luigi R.; Dotter, Aaron; Hempel, Maren; King, Ivan; Majewski, Steven; Milone, Antonino P.; Paust, Nathaniel; Reid, I. Neill

    2009-05-01

    The ACS Survey of Galactic Globular Clusters is a Hubble Space Telescope (HST) Treasury program designed to provide a new large, deep and homogeneous photometric database. Based on observations from this program, we have measured precise relative ages for a sample of 64 Galactic globular clusters by comparing the relative position of the clusters' main sequence turn offs, using main-sequence fitting to cross-compare clusters within the sample. This method provides relative ages to a formal precision of 2-7%. We demonstrate that the calculated relative ages are independent of the choice of theoretical model. We find that the Galactic globular cluster sample can be divided into two groups-a population of old clusters with an intrinsic age dispersion of ~3% and no age-metallicity relation, and a group of younger clusters with an age-metallicity relation similar to that of the globular clusters associated with the Sagittarius dwarf galaxy. These results are consistent with the Milky Way halo having formed in two phases. The first phase would be compatible with a rapid (<0.8 Gyr) assembling process of the halo, in which the clusters in the old group were formed. The second phase lasted much longer in time and resulted in a group of globular clusters with a clear age-metallicity relation. It is very tempting to argue that the origin of this second group of clusters is related to the accretion of Milky Way satellite galaxies, but the origin of the age-metallicity relation remains unclear.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. The Capsid Proteins of a Large, Icosahedral dsDNA Virus

    PubMed Central

    Yan, Xiaodong; Yu, Zeyun; Zhang, Ping; Battisti, Anthony J.; Chipman, Paul R.; Bajaj, Chandrajit; Bergoin, Max; Rossmann, Michael G.; Baker, Timothy S.

    2010-01-01

    Summary Chilo iridescent virus (CIV) is a large (~1850 Å diameter) insect virus with an icosahedral, T=147 capsid, a dsDNA genome, and an internal lipid membrane. The structure of CIV was determined to 13 Å resolution by means of cryo-electron microscopy (cryoEM) and three-dimensional image reconstruction. A homology model of P50, the CIV major capsid protein (MCP), was built based on its amino acid sequence and the structure of the homologous Paramecium bursaria chlorella virus 1 (PBCV-1) Vp54 MCP. This model was fitted into the cryoEM density for each of the 25 trimeric CIV capsomers per icosahedral asymmetric unit. A difference map, in which the fitted CIV MCP capsomers were subtracted from the CIV cryoEM reconstruction, showed that there are at least three different types of minor capsid proteins associated with the capsomers outside the lipid membrane. “Finger” proteins are situated at many, but not all, of the spaces between three adjacent capsomers within each trisymmetron, and “zip” proteins are situated between sets of three adjacent capsomers at the boundary between neighboring trisymmetrons and pentasymmetrons. Based on the results of segmentation and density correlations, there are at least eight finger proteins, and three dimeric and two monomeric zip proteins in one asymmetric unit of the CIV capsid. These minor proteins appear to stabilize the virus by acting as intercapsomer cross-links. One transmembrane “anchor” protein per icosahedral asymmetric unit, which extends from beneath one of the capsomers in the pentasymmetron to the internal leaflet of the lipid membrane, may provide additional stabilization for the capsid. These results are consistent with the observations for other large, icosahedral dsDNA viruses that also utilize minor capsid proteins for stabilization and determining their assembly. PMID:19027752

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Large protein-induced dipoles for a symmetric carotenoid in a photosynthetic antenna complex.

    PubMed

    Gottfried, D S; Steffen, M A; Boxer, S G

    1991-02-08

    Unusually large electric field effects have been measured for the absorption spectra of carotenoids (spheroidene) in the B800-850 light-harvesting complex from the photosynthetic bacterium Rhodobacter sphaeroides. Quantitative analysis shows that the difference in the permanent dipole moment between the ground state and excited states in this protein complex is substantially larger than for pure spheroidene extracted from the protein. The results demonstrate the presence of a large perturbation on the electronic structure of this nearly symmetric carotenoid due to the organized environment in the protein. This work also provides an explanation for the seemingly anomalous dependence of carotenoid band shifts on transmembrane potential and a generally useful approach for calibrating electric field-sensitive dyes that are widely used to probe potentials in biological systems.

  17. 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

  18. 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

  19. Revealing the global map of protein folding space by large-scale simulations

    NASA Astrophysics Data System (ADS)

    Sinner, Claude; Lutz, Benjamin; Verma, Abhinav; Schug, Alexander

    2015-12-01

    The full characterization of protein folding is a remarkable long-standing challenge both for experiment and simulation. Working towards a complete understanding of this process, one needs to cover the full diversity of existing folds and identify the general principles driving the process. Here, we want to understand and quantify the diversity in folding routes for a large and representative set of protein topologies covering the full range from all alpha helical topologies towards beta barrels guided by the key question: Does the majority of the observed routes contribute to the folding process or only a particular route? We identified a set of two-state folders among non-homologous proteins with a sequence length of 40-120 residues. For each of these proteins, we ran native-structure based simulations both with homogeneous and heterogeneous contact potentials. For each protein, we simulated dozens of folding transitions in continuous uninterrupted simulations and constructed a large database of kinetic parameters. We investigate folding routes by tracking the formation of tertiary structure interfaces and discuss whether a single specific route exists for a topology or if all routes are equiprobable. These results permit us to characterize the complete folding space for small proteins in terms of folding barrier ΔG‡, number of routes, and the route specificity RT.

  20. The DEAD box protein Mrh4 functions in the assembly of the mitochondrial large ribosomal subunit.

    PubMed

    De Silva, Dasmanthie; Fontanesi, Flavia; Barrientos, Antoni

    2013-11-05

    Proteins in a cell are universally synthesized by ribosomes. Mitochondria contain their own ribosomes, which specialize in the synthesis of a handful of proteins required for oxidative phosphorylation. The pathway of mitoribosomal biogenesis and factors involved are poorly characterized. An example is the DEAD box proteins, widely known to participate in the biogenesis of bacterial and cytoplasmic eukaryotic ribosomes as either RNA helicases or RNA chaperones, whose mitochondrial counterparts remain completely unknown. Here, we have identified the Saccharomyces cerevisiae mitochondrial DEAD box protein Mrh4 as essential for large mitoribosome subunit biogenesis. Mrh4 interacts with the 21S rRNA, mitoribosome subassemblies, and fully assembled mitoribosomes. In the absence of Mrh4, the 21S rRNA is matured and forms part of a large on-pathway assembly intermediate missing proteins Mrpl16 and Mrpl39. We conclude that Mrh4 plays an essential role during the late stages of mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    PubMed

    Howe, Kerstin; Schiffer, Philipp H; Zielinski, Julia; Wiehe, Thomas; Laird, Gavin K; Marioni, John C; Soylemez, Onuralp; Kondrashov, Fyodor; Leptin, Maria

    2016-04-01

    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. © 2016 The Authors.

  2. 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

  3. Extra-Large G Proteins Expand the Repertoire of Subunits in Arabidopsis Heterotrimeric G Protein Signaling1[OPEN

    PubMed Central

    Chakravorty, David; Gookin, Timothy E.; Milner, Matthew J.; Yu, Yunqing; Assmann, Sarah M.

    2015-01-01

    Heterotrimeric G proteins, consisting of Gα, Gβ, and Gγ subunits, are a conserved signal transduction mechanism in eukaryotes. However, G protein subunit numbers in diploid plant genomes are greatly reduced as compared with animals and do not correlate with the diversity of functions and phenotypes in which heterotrimeric G proteins have been implicated. In addition to GPA1, the sole canonical Arabidopsis (Arabidopsis thaliana) Gα subunit, Arabidopsis has three related proteins: the extra-large GTP-binding proteins XLG1, XLG2, and XLG3. We demonstrate that the XLGs can bind Gβγ dimers (AGB1 plus a Gγ subunit: AGG1, AGG2, or AGG3) with differing specificity in yeast (Saccharomyces cerevisiae) three-hybrid assays. Our in silico structural analysis shows that XLG3 aligns closely to the crystal structure of GPA1, and XLG3 also competes with GPA1 for Gβγ binding in yeast. We observed interaction of the XLGs with all three Gβγ dimers at the plasma membrane in planta by bimolecular fluorescence complementation. Bioinformatic and localization studies identified and confirmed nuclear localization signals in XLG2 and XLG3 and a nuclear export signal in XLG3, which may facilitate intracellular shuttling. We found that tunicamycin, salt, and glucose hypersensitivity and increased stomatal density are agb1-specific phenotypes that are not observed in gpa1 mutants but are recapitulated in xlg mutants. Thus, XLG-Gβγ heterotrimers provide additional signaling modalities for tuning plant G protein responses and increase the repertoire of G protein heterotrimer combinations from three to 12. The potential for signal partitioning and competition between the XLGs and GPA1 is a new paradigm for plant-specific cell signaling. PMID:26157115

  4. Rotary dialysis: its application to the preparation of large liposomes and large proteoliposomes (protein-lipid vesicles) with high encapsulation efficiency and efficient reconstitution of membrane proteins.

    PubMed

    Gould-Fogerite, S; Mannino, R J

    1985-07-01

    An apparatus for rotary dialysis is introduced and described in detail. The component parts are inexpensive, widely available, and relatively easy to modify and assemble. The apparatus achieves increased mixing of the contents of dialysis bags by constant end-over-end rotation. This technique is particularly useful in systems where maximum contact is desired between substances which would tend to partition under standard dialysis conditions. We have applied rotary dialysis to two liposome production methods. These are (i) the calcium-EDTA-chelation method of Papahadjopoulos et al. (1), which produces large unilamellar liposomes from negatively charged phospholipids, and (ii) a procedure for the reconstitution of membrane proteins into liposomes with a large internal aqueous space, which we have developed using the calcium-EDTA-chelation technique as a point of departure. In both techniques, vesicle formation occurs when a calcium-phospholipid precipitate is dissolved by the addition of EDTA. Instead of adding a 150 mM EDTA solution directly, as described in the original method, we have used overnight rotary dialysis against buffer containing 10 mM EDTA at the vesicle formation stage. Materials are encapsulated within the aqueous interior of the vesicles at much higher efficiencies when rotary dialysis is used in either method, compared to efficiencies obtained with direct addition of EDTA (up to 37% of added material vs a maximum published efficiency of 10% for direct addition). Rotary dialysis also promotes the reconstitution of a higher proportion of the membrane proteins present in the dialysis mixture into the bilayer of large liposomes (79 vs 41.6%). It also affects the content of liposomes qualitatively, allowing better reconstitution of the Sendai virus F glycoprotein than does direct addition of EDTA. These effects may be due to the slow time course, the extensive mixing of components, and the low volume-to-phospholipid ratios maintained during vesicle

  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. 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.

  7. Extremely α-Enriched Globular Clusters in Early-Type Galaxies:A Step toward the Dawn of Stellar Populations?

    NASA Astrophysics Data System (ADS)

    Puzia, Thomas H.; Kissler-Patig, Markus; Goudfrooij, Paul

    2006-09-01

    We compare [α/Fe], metallicity, and age distributions of globular clusters in elliptical, lenticular, and spiral galaxies, which we derive from Lick line index measurements. We find a large number of globular clusters in elliptical galaxies that reach significantly higher [α/Fe] values ([α/Fe]>0.5) than any clusters in lenticular and spiral galaxies. Most of these extremely α-enriched globular clusters are old (t>8 Gyr), and cover the metallicity range -1<~[Z/H]<~0. A comparison with supernova yield models suggests that the progenitor gas clouds of these globular clusters must have been predominantly enriched by massive stars (>~20 Msolar), with little contribution from lower mass stars. The measured [α/Fe] ratios are also consistent with yields of very massive pair-instability supernovae (~130-190 Msolar). Both scenarios imply that the chemical enrichment of the progenitor gas was completed on extremely short timescales of the order of a few Myr. Given the lower [α/Fe] average ratios of the diffuse stellar population in early-type galaxies, our results suggest that these extremely α-enhanced globular clusters could be members of the very first generation of star clusters formed, and that their formation epochs would predate the formation of the majority of stars in giant early-type galaxies.

  8. 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.

  9. 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.

  10. 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

  11. Modeling Black Holes in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Ivanova, Natalia

    2013-04-01

    I will review the current theoretical understanding of what is the population of black holes in globular clusters, as well as challenges in their modeling. Black hole binaries are the tip of the iceberg, and our best link to observations. In a dense stellar environment, such binaries are formed via dynamical encounters. The analyses show that the formation path of black hole X-ray binaries is very different from the well-known formation channels for neutron star X-ray binaries, like binary exchanges and physical collisions. This formation path is composed of several distinct formation stages, where the most crucial one is triple-induced mass transfer.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. Limits on WIMPs from globular cluster stars

    NASA Astrophysics Data System (ADS)

    Rood, R. T.; Renzini, A.

    The theoretical model proposed by Spergel and Faulkner (1988) to explain the observed solar neutrino flux is tested by applying it to detailed stellar models based on data for globular-cluster stars. In this model, nonbaryonic weakly interacting massive particles (WIMPs) act to transport energy in an isothermal central solar core, where B-8 neutrinos are produced. The potential effects of WIMPs on stellar evolution in the main sequence, the subgiant branch, near the red-giant tip, and on the horizontal branch are discussed, and effects which should be observable are identified. For the horizontal-branch stars, a diagram showing severe observational constraints on WIMP physical parameters is presented.

  18. 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

  19. 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].

  20. 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.

  1. Dynamical Formation of Black Hole Binaries in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Rasio, Frederic A.; Chatterjee, Sourav; Kremer, Kyle; Rodriguez, Carl

    2017-08-01

    Theoretical predictions for black holes in field populations of binary stars are extremely sensitive to the assumptions of stellar evolution, leading, for example, to predicted merger rates for binary black holes that span several orders of magnitude. But in dense stellar environments such as globular clusters, binary black holes form by well-understood gravitational interactions. We will present an overview of recent theoretical work on the dynamical formation of black hole binaries based on realistic N-body simulations of globular clusters. By calibrating theoretical models against observed properties of globular clusters, we find that the mergers of dynamically formed binaries could eventually be detected by Advanced LIGO at a rate of at least ~ 100 per year, potentially dominating the overall detection rate of gravitational wave sources. Dynamical processes in globular clusters can also form very naturally the black hole X-ray binaries that have been tentatively identified recently in many Milky Way and extragalactic globular clusters.

  2. Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase.

    PubMed

    Ye, Xinhao; Zhang, Chenming; Zhang, Y-H Percival

    2012-06-01

    The Clostridium thermocellum cellobiose phosphorylase (CtCBP) is a large protein consisting of 812 amino acids and has great potential in the production of sugar phosphates, novel glycosides, and biofuels. It is relatively stable at 50 °C, but is rapidly inactivated at 70 °C. To stabilize CtCBP at elevated temperatures, two protein-engineering approaches were applied, i.e. site-directed mutagenesis based on structure-guided homology analysis and random mutagenesis at various mutation rates. The former chose substitutions by comparison of the protein sequences of CBP homologs, utilized structural information to identify key amino acid residues responsible for enhanced stability, and then created a few variants accurately. The latter constructed large libraries of random mutants at different mutagenesis frequencies. A novel combinational selection/screening strategy was employed to quickly isolate thermostability-enhanced and active variants. Several stability-enhanced mutants were obtained by both methods. Manually combining the stabilizing mutations identified from both rational and random approaches led to the best mutant (CM3) with the halftime of inactivation at 70 °C extended from 8.3 to 24.6 min. The temperature optimum of CM3 was increased from 60 to 80 °C. These results suggested that a combination of rational design and random mutagenesis could have a solid basis for engineering large proteins.

  3. 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.

  4. 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

  5. A Semi-Automated Assignment Protocol for Methyl Group Side-Chains in Large Proteins

    PubMed Central

    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 semi-empirical 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 NOEs and 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. PMID:26791975

  6. A Semi