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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. Accelerated simulation of unfolding and refolding of a large single chain globular protein

    PubMed Central

    Seddon, Gavin M.; Bywater, Robert P.

    2012-01-01

    We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs Concoord and Darvols. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work. PMID:22870389

  4. Accelerated simulation of unfolding and refolding of a large single chain globular protein.

    PubMed

    Seddon, Gavin M; Bywater, Robert P

    2012-07-01

    We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs Concoord and Darvols. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work. PMID:22870389

  5. 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

  6. On the cold denaturation of globular proteins

    NASA Astrophysics Data System (ADS)

    Ascolese, Eduardo; Graziano, Giuseppe

    2008-12-01

    The recent finding that yeast frataxin shows, at pH 7.0, cold denaturation at 274 K and hot denaturation at 303 K [A. Pastore, S.R. Martin, A. Politou, K.C. Kondapalli, T. Stemmler, P.A. Temussi, J. Am. Chem. Soc. 129 (2007) 5374] calls for a deeper rationalization of the molecular mechanisms stabilizing-destabilizing the native state of globular proteins. It is shown that the statistical thermodynamic model originally developed by Ikegami can reproduce in a more-than-qualitative manner the two conformational transitions of yeast frataxin, providing important clues on their molecular origin.

  7. 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

  8. 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.

  9. Universality of vibrational spectra of globular proteins.

    PubMed

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

    2016-02-23

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

  10. Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization

    PubMed Central

    Berezovsky, Igor N.

    2002-01-01

    Structural and functional complexity of proteins is dramatically reduced to a simple linear picture when the laws of polymer physics are considered. A basic unit of the protein structure is a nearly standard closed loop of 25–35 amino acid residues, and every globular protein is built of consecutively connected closed loops. The physical necessity of the closed loops had been apparently imposed on the early stages of protein evolution. Indeed, the most frequent prototype sequence motifs in prokaryotic proteins have the same sequence size, and their high match representatives are found as closed loops in crystallized proteins. Thus, the linear organization of the closed loop elements is a quintessence of protein evolution, structure and folding. PMID:18629251

  11. 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.

  12. 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. PMID:24654888

  13. 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).

  14. Macromolecular crowding fails to fold a globular protein in cells.

    PubMed

    Schlesinger, Alexander P; Wang, Yaqiang; Tadeo, Xavier; Millet, Oscar; Pielak, Gary J

    2011-06-01

    Proteins perform their functions in cells where macromolecular solutes reach concentrations of >300 g/L and occupy >30% of the volume. The volume excluded by these macromolecules stabilizes globular proteins because the native state occupies less space than the denatured state. Theory predicts that crowding can increase the ratio of folded to unfolded protein by a factor of 100, amounting to 3 kcal/mol of stabilization at room temperature. We tested the idea that volume exclusion dominates the crowding effect in cells using a variant of protein L, a 7 kDa globular protein with seven lysine residues replaced by glutamic acids; 84% of the variant molecules populate the denatured state in dilute buffer at room temperature, compared with 0.1% for the wild-type protein. We then used in-cell NMR spectroscopy to show that the cytoplasm of Escherichia coli does not overcome even this modest (∼1 kcal/mol) free-energy deficit. The data are consistent with the idea that nonspecific interactions between cytoplasmic components can overcome the excluded-volume effect. Evidence for these interactions is provided by the observations that adding simple salts folds the variant in dilute solution but increasing the salt concentration inside E. coli does not fold the protein. Our data are consistent with the results of other studies of protein stability in cells and suggest that stabilizing excluded-volume effects, which must be present under crowded conditions, can be ameliorated by nonspecific interactions between cytoplasmic components.

  15. 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

  16. Dynamic prestress in a globular protein.

    PubMed

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

    2012-01-01

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

  17. Microwave-enhanced folding and denaturation of globular proteins

    NASA Astrophysics Data System (ADS)

    Bohr, Henrik; Bohr, Jakob

    2000-04-01

    It is shown that microwave irradiation can affect the kinetics of the folding process of some globular proteins, especially β-lactoglobulin. At low temperature the folding from the cold denatured phase of the protein is enhanced, while at a higher temperature the denaturation of the protein from its folded state is enhanced. In the latter case, a negative temperature gradient is needed for the denaturation process, suggesting that the effects of the microwaves are nonthermal. This supports the notion that coherent topological excitations can exist in proteins. The application of microwaves hold promises for a wide range of biotechnological applications, such as protein synthesis, protein aggregation, etc., and may have implications for biological systems as well.

  18. 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.

  19. 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.

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

    DOE PAGES

    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 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

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

    PubMed

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

    2016-04-01

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

  2. 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. PMID:27498593

  3. Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins.

    PubMed

    Maiorov, V N; Crippen, G M

    1994-01-14

    In the study of globular protein conformations, one customarily measures the similarity in three-dimensional structure by the root-mean-square deviation (RMSD) of the C alpha atomic coordinates after optimal rigid body superposition. Even when the two protein structures each consist of a single chain having the same number of residues so that the matching of C alpha atoms is obvious, it is not clear how to interpret the RMSD. A very large value means they are dissimilar, and zero means they are identical in conformation, but at what intermediate values are they particularly similar or clearly dissimilar? While many workers in the field have chosen arbitrary cutoffs, and others have judged values of RMSD according to the observed distribution of RMSD for random structures, we propose a self-referential, non-statistical standard. We take two conformers to be intrinsically similar if their RMSD is smaller than that when one of them is mirror inverted. Because the structures considered here are not arbitrary configurations of point atoms, but are compact, globular, polypeptide chains, our definition is closely related to similarity in radius of gyration and overall chain folding patterns. Being strongly similar in our sense implies that the radii of gyration must be nearly identical, the root-mean-square deviation in interatomic distances is linearly related to RMSD, and the two chains must have the same general fold. Only when the RMSD exceeds this level can parts of the polypeptide chain undergo nontrivial rearrangements while remaining globular. This enables us to judge when a prediction of a protein's conformation is "correct except for minor perturbations", or when the ensemble of protein structures deduced from NMR experiments are "basically in mutual agreement". PMID:8289285

  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. 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.

  6. Translational and rotational diffusion of a small globular protein under crowded conditions.

    PubMed

    Li, Conggang; Wang, Yaqiang; Pielak, Gary J

    2009-10-01

    Protein-protein interaction is the fundamental step of biological signal transduction. Interacting proteins find each other by diffusion. To gain insight into diffusion under the crowded conditions found in cells, we used nuclear magnetic resonance spectroscopy (NMR) to measure the effects of solvent additives on the translational and rotational diffusion of the 7.4 kDa globular protein, chymotrypsin inhibitor 2. The additives were glycerol and the macromolecular crowding agent, polyvinyl pyrrolidone (PVP). Both translational diffusion and rotational diffusion decrease with increasing solution viscosity. For glycerol, the decrease obeys the Stokes-Einstein and Stokes-Einstein Debye laws. Three types of deviation are observed for PVP: the decrease in diffusion with increased viscosity is less than predicted, this negative deviation is greater for rotational diffusion, and the negative deviation increases with increasing PVP molecular weight. We discuss our results in terms of other studies on the effects of macromolecules on globular protein diffusion.

  7. Morphology and phase separation of hydrophobic clusters of soy globular protein polymers.

    PubMed

    Sun, Xiuzhi Susan; Wang, Donghai; Zhang, Lu; Mo, Xiaoqun; Zhu, Li; Bolye, Dan

    2008-04-01

    Protein hydrophobic interaction has been considered the most important factor dominating protein folding, aggregation, gelling, self-assembly, adhesion, and cohesion properties. In this paper, morphology and phase separation of hydrophobic clusters, networks, and aggregates of soy globular protein polymers, induced by using a reducing agent (NaHSO3), are studied using microscopic instruments. The morphology and phase separation of these hydrophobic clusters are sensitive to protein structure and composition, pH, and ionic-strength (I(m)). Most of the clusters are in spherical-shape architecture and mainly consist of hydrophobic polypeptides. Rod-shape clusters were also observed at higher ionic strength, and mainly consist of hydrophilic polypeptides. The ratio of hydrophobic/hydrophilic (HB/HL) polypeptides is important to facilitate the formation of clusters in an environment with a certain pH value and ionic strength. At HB/HL 0.8, uniform spherical clusters were observed and diameters ranged from 30 to 70 nm. At HB/HL <0.8, large spherical clusters were formed with diameters ranging from 100 to 1,000 nm, and at HB/HL >or=1.8, large hydrophobic aggregates formed, and size of aggregates can be up to 2 500 nm. When solid content increased from 3% to 38%, at I(m) or= 0.115 mol x L(-1), HB/HL ratio >or=1.8, the large aggregates became very cohesive and viscoelastic. Clear phase separation was observed during curing between hydrophobic and hydrophilic protein polymers. Phase-separation degree increased as HB/HL ratio increased.

  8. 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.

  9. Cooperative charge fluctuations by migrating protons in globular proteins.

    PubMed

    Careri, G

    1998-01-01

    A review of the hydrogen bonded network on the protein surface shows the presence of a charged complex system with parallel and competitive interactions, including ionizable side-chains, migrating protons, bound water and nearby backbone peptides. This system displays cooperative effects of dynamical nature, reviewed for lysozyme as a case. By increasing the water coverage of the protein powder, the bound water cluster exhibits a percolative transition, detectable by the onset of large water-assisted displacements of migrating protons, with a parallel emergence of protein mobility and biological function. By lowering the temperature, migrating protons exhibit a glassy dielectric relaxation in the low frequency range, pointing to a frustration by competing interactions similar to that observed in spin glasses and fragile glass forming liquids. The observation of these dissipative processes implies the occurrence of spontaneous charge fluctuations. A simplified model of the protein surface, where conformational and ionizable side-chain fluctuations are averaged out, is used to discuss the statistical physics of these cooperative effects. Some biological implications of this dynamical cooperativity for enzymatic activity are briefly suggested at the end.

  10. 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

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

    PubMed Central

    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 ES(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 ES(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 ES(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 ES(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. PMID:25988167

  12. [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.

  13. The effect of the presence of globular proteins and elongated polymers on enzyme activity.

    PubMed

    Derham, Barry K; Harding, John J

    2006-06-01

    We have studied the effect of a crowded (macromolecular) solution on reaction rates of the decarboxylating enzymes urease, pyruvate decarboxylase and glutamate decarboxylase. A variety of crowding agents were used including haemoglobin, lysozyme, various dextrans and polyethylene glycol. Enzyme reaction rates of all three enzymes show two different types of effect that separate the globular proteins from the polysaccharides/polymers. Increasing concentration of globular proteins caused a dramatic rise in enzyme activity up to 30% crowding concentration then the activity decreased, whereas the polymers caused a concentration dependent decrease in activity. The viscosities of the globular proteins were low compared to the polymers. The increased activity with proteins may be due to the decreased amount of free water, which leads to higher effective concentration of substrates, or to an increased oligomeric state by self-association. The lower activities of all enzymes with all agents at high concentrations may be explained by a decrease in rates of diffusion. An increase in protein crowding (decrease in cell water content) may contribute to pathological conditions including cataract and Alzheimer's disease.

  14. 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

  15. 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.

  16. 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).

  17. Measurement of Globular Protein Molecules by Electron Microscopy

    PubMed Central

    Hall, Cecil E.

    1960-01-01

    A series of molecular species with approximately spherical shape and with molecular weights between 35,000 and 250,000 were shadowed with platinum while resting on a cleaved mica surface. They were backed, stripped from the surface, and examined by electron microscopy. Materials examined were: pepsin, liver alcohol dehydrogenase, yeast alcohol dehydrogenase, glutamic dehydrogenase, polyhedral virus protein (insect), fibrinogen substructure, alkaline phosphatase, and microsomal particles from Escherichia coli. Measurements were made of widths perpendicular to the shadowing direction and heights were deduced from shadow lengths. For those molecular species with well established molecular weights the average heights correlate very well with the diameter of the theoretical sphere but the average widths are too great by 50 to 80 A due to the lateral growth of the deposited metal. Although the distortion in shape of shadowed particles is relatively large, with standardized conditions for shadowing, it is possible to make allowance for the distortion and to obtain reasonably reliable estimates of the dimensions of spherical organic particles down to a molecular weight of about 35,000. PMID:14399016

  18. Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions.

    PubMed Central

    Bahar, I; Jernigan, R L

    1994-01-01

    On-lattice simulations of two-dimensional self-avoiding chains subject to homogeneous intramolecular attractive interactions were performed as a model for studying various density regimes in globular proteins. For short chains of less than 15 units, all conformations were generated and classified by density. The range of intramolecular interactions was found to increase uniformly with density, and the average number of topological contacts is directly proportional to density. The uniform interaction energy increases the probability of high density states but does not necessarily lead to dominance of the highest density state. Typically, several large peaks appear in the probability distribution of packing densities, their location and amplitude being determined by the balance between entropic effects enhancing more expanded conformations and attractive interactions favoring compact forms. Also, the homogeneous interaction energy affects the distribution of most probable interacting points in favor of the longer range interactions over the short range ones, but in addition it introduces some more detailed preferences even among short range interactions. There are some implications about the characteristics of the intermediate density states and also for the likelihood that the native state does not correspond completely to the lowest energy conformation. Images FIGURE 7 FIGURE 8 FIGURE 9 FIGURE 10 FIGURE 11 FIGURE 12 FIGURE 13 PMID:8161699

  19. 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.

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

    PubMed Central

    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. PMID:24748753

  1. Globular Protein Folding In Vitro and In Vivo.

    PubMed

    Gruebele, Martin; Dave, Kapil; Sukenik, Shahar

    2016-07-01

    In vitro, computational, and theoretical studies of protein folding have converged to paint a rich and complex energy landscape. This landscape is sensitively modulated by environmental conditions and subject to evolutionary pressure on protein function. Of these environments, none is more complex than the cell itself, where proteins function in the cytosol, in membranes, and in different compartments. A wide variety of kinetic and thermodynamics experiments, ranging from single-molecule studies to jump kinetics and from nuclear magnetic resonance to imaging on the microscope, have elucidated how protein energy landscapes facilitate folding and how they are subject to evolutionary constraints and environmental perturbation. Here we review some recent developments in the field and refer the reader to some original work and additional reviews that cover this broad topic in protein science. PMID:27391927

  2. 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; Zhang, Yang; Kim, Chansoo; Faraone, Antonio; Fratini, Emiliano; Baglioni, Piero

    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

  3. Radially softening diffusive motions in a globular protein.

    PubMed

    Dellerue, S; Petrescu, A J; Smith, J C; Bellissent-Funel, M C

    2001-09-01

    Molecular dynamics simulation, quasielastic neutron scattering and analytical theory are combined to characterize diffusive motions in a hydrated protein, C-phycocyanin. The simulation-derived scattering function is in approximate agreement with experiment and is decomposed to determine the essential contributions. It is found that the geometry of the atomic motions can be modeled as diffusion in spheres with a distribution of radii. The time dependence of the dynamics follows stretched exponential behavior, reflecting a distribution of relaxation times. The average side chain and backbone dynamics are quantified and compared. The dynamical parameters are shown to present a smooth variation with distance from the core of the protein. Moving outward from the center of the protein there is a progressive increase of the mean sphere size, accompanied by a narrowing and shifting to shorter times of the relaxation time distribution. This smooth, "radially softening" dynamics may have important consequences for protein function. It also raises the possibility that the dynamical or "glass" transition with temperature observed experimentally in proteins might be depth dependent, involving, as the temperature decreases, progressive freezing out of the anharmonic dynamics with increasing distance from the center of the protein.

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

    PubMed

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

    2015-06-01

    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). PMID:25965109

  5. 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.

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

    PubMed

    Chuev, G N; Lakhno, V D

    1993-07-01

    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.

  7. 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.

  8. Creep anomaly in electrospun fibers made of globular proteins.

    PubMed

    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. PMID:24483479

  9. 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.

  10. 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.

  11. Discriminating compact nonnative structures from the native structure of globular proteins.

    PubMed Central

    Wang, Y; Zhang, H; Li, W; Scott, R A

    1995-01-01

    Prediction of the native tertiary structure of a globular protein from the primary sequence will require a potential energy model that can discriminate all nonnative structures from the native structure(s). A successful model must distinguish not only alternate structures that are very nonnative but also alternate structures that are compact and near-native. We describe here a method, based on molecular dynamics simulation, that allows generation of hundreds of compact alternate structures that are arbitrarily close to the native structure. In this way, a significant amount of conformational space in the neighborhood of the native structure can be sampled and these alternate structures can be used as a stringent test of protein folding models. We have used two sets of these alternate structures generated for six crystallographically characterized small globular proteins (1200 alternate structures in all) to test eight empirical energy models for their ability to discriminate alternate from native structures. Seven of the models fail to correctly identify at least some of the alternate structures as nonnative. An atomic solvation model is presented that succeeds in discriminating all 1200 alternate structures from native. Images Fig. 1 PMID:7846040

  12. Coil fraction-dependent phase behaviour of a model globular protein-polymer diblock copolymer.

    PubMed

    Thomas, Carla S; Olsen, Bradley D

    2014-05-01

    The self-assembly of the model globular protein-polymer block copolymer mCherry-b-poly(N-isopropyl acrylamide) is explored across a range of polymer coil fractions from 0.21 to 0.82 to produce a phase diagram for these materials as a function of molecular composition. Overall, four types of morphologies were observed: hexagonally packed cylinders, perforated lamellae, lamellae, and disordered nanostructures. Across all coil fractions and morphologies, a lyotropic re-entrant order-disorder transition in water was observed, with disordered structures below 30 wt% and above 70 wt% and well-ordered morphologies at intermediate concentrations. Solid state samples prepared by solvent evaporation show moderately ordered structures similar to those observed in 60 wt% solutions, suggesting that bulk structures result from kinetic trapping of morphologies which appear at lower concentrations. While highly ordered cylindrical nanostructures are observed around a bioconjugate polymer volume fraction of 0.3 and well-ordered lamellae are seen near a volume fraction of 0.6, materials at lower or higher coil fractions become increasingly disordered. Notable differences between the phase behaviour of globular protein-polymer block copolymers and coil-coil diblock copolymers include the lack of spherical nanostructures at either high or low polymer coil fractions as well as shifted phase boundaries between morphologies which result in an asymmetric phase diagram. PMID:24695642

  13. Effect of a low-frequency magnetic field on the structure of globular blood proteins

    NASA Astrophysics Data System (ADS)

    Zalesskaya, G. A.; Ulashchik, V. S.; Mit'kovskaya, N. P.; Laskina, O. V.; Kuchinskii, A. V.

    2007-09-01

    We used IR Fourier absorption spectra of blood to study changes in the structure of globular blood proteins with extracorporeal autohemomagnetotherapy, used to treat ischemic heart disease. We compare the spectra of blood before and after magnetotherapy in the regions: amide I (1655 cm-1), amide II (1545 cm-1), amide III (1230-1350 cm-1), amide IV and amide V (400-700 cm-1). We have shown that pronounced changes in the spectra in the indicated regions on direct exposure of blood in vivo to a low-frequency pulsed magnetic field are connected with conformational changes in the secondary structure of globular blood proteins, which are apparent in the increase in the contribution of the α-helix conformation. We discuss the magnetotherapy-initiated appearance of new IR absorption bands at 1018 and 1038 cm-1 and an increase in the intensity of a number of other bands located in the 1000-1200 cm-1 region, which suggests a change in the concentration of some blood components.

  14. 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

  15. 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. PMID:22924842

  16. 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.

  17. [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.

  18. A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

    PubMed Central

    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). PMID:23326595

  19. Predicting the activity coefficients of free-solvent for concentrated globular protein solutions using independently determined physical parameters.

    PubMed

    McBride, Devin W; Rodgers, Victor G J

    2013-01-01

    The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations.

  20. 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.

  1. Unusual dynamics of concentration fluctuations in solutions of weakly attractive globular proteins.

    PubMed

    Bucciarelli, Saskia; Casal-Dujat, Lucía; De Michele, Cristiano; Sciortino, Francesco; Dhont, Jan; Bergenholtz, Johan; Farago, Bela; Schurtenberger, Peter; Stradner, Anna

    2015-11-19

    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.

  2. Unusual dynamics of concentration fluctuations in solutions of weakly attractive globular proteins.

    PubMed

    Bucciarelli, Saskia; Casal-Dujat, Lucía; De Michele, Cristiano; Sciortino, Francesco; Dhont, Jan; Bergenholtz, Johan; Farago, Bela; Schurtenberger, Peter; Stradner, Anna

    2015-11-19

    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

  3. Do the Large Magellanic Cloud and Milky Way Globular Clusters Share a Common Origin?

    NASA Astrophysics Data System (ADS)

    Tucker, Bradley E.; Olsen, K. A.; Blum, B.

    2006-12-01

    We obtained infrared spectroscopy between 1.5552 and 1.5600 microns, of six metal poor red giant stars in NGC 2019, a globular cluster in the LMC, with the Phoenix high-resolution spectrograph at the 8.1-m Gemini South telescope. Current [Fe/H] estimates, based on medium-resolution Ca-triplet spectroscopy and CMD-fitting, disagree by 0.6 dex. In addition, studies of the LMC's globular cluster system performed with the Hubble Space Telescope suggest that the LMC and Milky Way globular clusters have ages within 1 Gyr of each other. Spectral synthesis was carried out in order to calculate accurate oxygen and iron abundances. We used V and I photometry in conjunction with Padova stellar isochrones to calculate the stellar effective temperatures, bolometric corrections, gravities, and luminosities. We were not able to independently measure the microturbulent velocities, and so they were estimated using stellar luminosities and gravities. Preliminary analysis shows a mean [O/Fe] of 0.35 ± .10 for NGC 2019, which is similar to values found in old globular clusters of the Milky Way.

  4. Beyond the Brim of the Hat: Kinematics of Globular Clusters out to Large Radii in the Sombrero Galaxy

    NASA Astrophysics Data System (ADS)

    Dowell, Jessica L.; Rhode, Katherine L.; Bridges, Terry J.; Zepf, Stephen E.; Gebhardt, Karl; Freeman, Ken C.; de Boer, Elizabeth Wylie

    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 ~5Re ), 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 ~9Re ). 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/LV increases from 4.5 at the center to a value of 20.9 at 41 kpc (~9Re 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 (~4Re 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.

  5. 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.

  6. 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.

  7. Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions.

    PubMed

    Gomes, Antonio L C; de Rezende, Júlia R; Pereira de Araújo, Antônio F; Shakhnovich, Eugene I

    2007-02-01

    We perform a statistical analysis of atomic distributions as a function of the distance R from the molecular geometrical center in a nonredundant set of compact globular proteins. The number of atoms increases quadratically for small R, indicating a constant average density inside the core, reaches a maximum at a size-dependent distance R(max), and falls rapidly for larger R. The empirical curves turn out to be consistent with the volume increase of spherical concentric solid shells and a Fermi-Dirac distribution in which the distance R plays the role of an effective atomic energy epsilon(R) = R. The effective chemical potential mu governing the distribution increases with the number of residues, reflecting the size of the protein globule, while the temperature parameter beta decreases. Interestingly, betamu is not as strongly dependent on protein size and appears to be tuned to maintain approximately half of the atoms in the high density interior and the other half in the exterior region of rapidly decreasing density. A normalized size-independent distribution was obtained for the atomic probability as a function of the reduced distance, r = R/R(g), where R(g) is the radius of gyration. The global normalized Fermi distribution, F(r), can be reasonably decomposed in Fermi-like subdistributions for different atomic types tau, F(tau)(r), with Sigma(tau)F(tau)(r) = F(r), which depend on two additional parameters mu(tau) and h(tau). The chemical potential mu(tau) affects a scaling prefactor and depends on the overall frequency of the corresponding atomic type, while the maximum position of the subdistribution is determined by h(tau), which appears in a type-dependent atomic effective energy, epsilon(tau)(r) = h(tau)r, and is strongly correlated to available hydrophobicity scales. Better adjustments are obtained when the effective energy is not assumed to be necessarily linear, or epsilon(tau)*(r) = h(tau)*r(alpha,), in which case a correlation with hydrophobicity

  8. Numerical study of a binary Yukawa model in regimes characteristic of globular proteins in solutions

    SciTech Connect

    Giacometti, Achille; Gazzillo, Domenico; Pastore, Giorgio; Das, Tushar Kanti

    2005-03-01

    The main goal of this paper is to assess the limits of validity, in the regime of low concentration and strong Coulomb coupling (high molecular charges), of a simple perturbative approximation to the radial distribution functions (RDF's), based upon a low-density expansion of the potential of mean force and proposed to describe protein-protein interactions in a recent small-angle-scattering (SAS) experimental study. A highly simplified Yukawa (screened Coulomb) model of monomers and dimers of a charged globular protein ({beta}-lactoglobulin) in solution is considered. We test the accuracy of the RDF approximation, as a necessary complementary part of the previous experimental investigation, by comparison with the fluid structure predicted by approximate integral equations and exact Monte Carlo (MC) simulations. In the MC calculations, an Ewald construction for Yukawa potentials has been used to take into account the long-range part of the interactions in the weakly screened cases. Our results confirm that the perturbative first-order approximation is valid for this system even at strong Coulomb coupling, provided that the screening is not too weak (i.e., for Debye length smaller than monomer radius). A comparison of the MC results with integral equation calculations shows that both the hypernetted-chain (HNC) and Percus-Yevick closures have a satisfactory behavior under these regimes, with the HNC being superior throughout. The relevance of our findings for interpreting SAS results is also discussed.

  9. 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

  10. 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

  11. 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

  12. Artificial Golgi apparatus: globular protein-like dendrimer facilitates fully automated enzymatic glycan synthesis.

    PubMed

    Matsushita, Takahiko; Nagashima, Izuru; Fumoto, Masataka; Ohta, Takashi; Yamada, Kuriko; Shimizu, Hiroki; Hinou, Hiroshi; Naruchi, Kentaro; Ito, Takaomi; Kondo, Hirosato; Nishimura, Shin-Ichiro

    2010-11-24

    Despite the growing importance of synthetic glycans as tools for biological studies and drug discovery, a lack of common methods for the routine synthesis remains a major obstacle. We have developed a new method for automated glycan synthesis that employs the enzymatic approach and a dendrimer as an ideal support within the chemical process. Recovery tests using a hollow fiber ultrafiltration module have revealed that monodisperse G6 (MW = 58 kDa) and G7 (MW = 116 kDa) poly(amidoamine) dendrimers exhibit a similar profile to BSA (MW = 66 kDa). Characteristics of the globular protein-like G7 dendrimer with high solubility and low viscosity in water greatly enhanced throughput and efficiency in automated synthesis while random polyacrylamide-based supports entail significant loss during the repetitive reaction/separation step. The present protocol allowed for the fully automated enzymatic synthesis of sialyl Lewis X tetrasaccharide derivatives over a period of 4 days in 16% overall yield from a simple N-acetyl-d-glucosamine linked to an aminooxy-functionalized G7 dendrimer.

  13. Artificial Golgi apparatus: globular protein-like dendrimer facilitates fully automated enzymatic glycan synthesis.

    PubMed

    Matsushita, Takahiko; Nagashima, Izuru; Fumoto, Masataka; Ohta, Takashi; Yamada, Kuriko; Shimizu, Hiroki; Hinou, Hiroshi; Naruchi, Kentaro; Ito, Takaomi; Kondo, Hirosato; Nishimura, Shin-Ichiro

    2010-11-24

    Despite the growing importance of synthetic glycans as tools for biological studies and drug discovery, a lack of common methods for the routine synthesis remains a major obstacle. We have developed a new method for automated glycan synthesis that employs the enzymatic approach and a dendrimer as an ideal support within the chemical process. Recovery tests using a hollow fiber ultrafiltration module have revealed that monodisperse G6 (MW = 58 kDa) and G7 (MW = 116 kDa) poly(amidoamine) dendrimers exhibit a similar profile to BSA (MW = 66 kDa). Characteristics of the globular protein-like G7 dendrimer with high solubility and low viscosity in water greatly enhanced throughput and efficiency in automated synthesis while random polyacrylamide-based supports entail significant loss during the repetitive reaction/separation step. The present protocol allowed for the fully automated enzymatic synthesis of sialyl Lewis X tetrasaccharide derivatives over a period of 4 days in 16% overall yield from a simple N-acetyl-d-glucosamine linked to an aminooxy-functionalized G7 dendrimer. PMID:21033706

  14. 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.

  15. Globular and disordered—the non-identical twins in protein-protein interactions

    PubMed Central

    Teilum, Kaare; Olsen, Johan G.; Kragelund, Birthe B.

    2015-01-01

    In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol−1. PMID:26217672

  16. 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. PMID:26574230

  17. 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.

  18. 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.

  19. Low-Frequency Modes of Peptides and Globular Proteins in Solution Observed by Ultrafast OHD-RIKES Spectroscopy

    PubMed Central

    Giraud, Gerard; Karolin, Jan; Wynne, Klaas

    2003-01-01

    The low-frequency (1–200 cm−1) vibrational spectra of peptides and proteins in solution have been investigated with ultrafast optical heterodyne-detected Raman-induced Kerr-effect spectroscopy (OHD-RIKES). Spectra have been obtained for di-L-alanine (ALA(2)) and the α-helical peptide poly-L-alanine (PLA) in dichloroacetic acid solution. The poly-L-alanine spectrum shows extra amplitude compared to the di-L-alanine spectrum, which can be explained by the secondary structure of the former. The globular proteins lysozyme, α-lactalbumin, pepsin, and β-lactoglobulin in aqueous solution have been studied to determine the possible influence of secondary or tertiary structure on the low-frequency spectra. The spectra of the globular proteins have been analyzed in terms of three nondiffusive Brownian oscillators. The lowest frequency oscillator corresponds to the so-called Boson peak observed in inelastic neutron scattering (INS). The remaining two oscillators are not observed in inelastic neutron scattering, do therefore not involve significant motion of hydrogen atoms, and may be associated with delocalized backbone torsions. PMID:12944303

  20. Evidence that complement protein C1q interacts with C-reactive protein through its globular head region.

    PubMed

    McGrath, Fabian D G; Brouwer, Mieke C; Arlaud, Gérard J; Daha, Mohamed R; Hack, C Erik; Roos, Anja

    2006-03-01

    C1q acts as the recognition unit of the first complement component, C1, and binds to immunoglobulins IgG and IgM, as well as to non-Ig ligands, such as C-reactive protein (CRP). IgG and IgM are recognized via the globular head regions of C1q (C1qGR), whereas CRP has been postulated to interact with the collagen-like region (C1qCLR). In the present study, we used a series of nine mAbs to C1q, five directed against C1qGR and four against C1qCLR, to inhibit the interaction of C1q with CRP. The F(ab')(2) of each of the five mAbs directed against C1qGR inhibited binding of C1q to polymerized IgG. These five mAbs also successfully inhibited the interaction of C1q with CRP. Moreover, these five mAbs inhibited C1 activation by CRP as well as by polymerized IgG in vitro. In contrast, none of the four mAbs against C1qCLR inhibited C1q interaction with CRP or IgG, or could reduce activation of complement by CRP or polymerized IgG. These results provide the first evidence that the interaction of C1q with CRP or IgG involves sites located in the C1qGR, whereas sites in the CLR do not seem to be involved in the physiological interaction of C1q with CRP.

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

    PubMed Central

    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. PMID:26325194

  2. 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

    Kathuria, Sagar V; Chan, Yvonne H; Nobrega, R Paul; Özen, Ayşegül; Matthews, C Robert

    2016-03-01

    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.

  3. THE EXTENDED MAIN-SEQUENCE TURNOFF CLUSTERS OF THE LARGE MAGELLANIC CLOUD-MISSING LINKS IN GLOBULAR CLUSTER EVOLUTION

    SciTech Connect

    Keller, Stefan C.; Mackey, A. Dougal; Da Costa, Gary S.

    2011-04-10

    Recent observations of intermediate-age (1-3 Gyr) massive star clusters in the Large Magellanic Cloud have revealed that the majority possess bifurcated or extended main-sequence turnoff (EMSTO) morphologies. This effect can be understood to arise from subsequent star formation among the stellar population with age differences between constituent stars amounting to 50-300 Myr. Age spreads of this order are similarly invoked to explain the light-element abundance variations witnessed in ancient globular clusters (GCs). In this paper, we explore the proposition that the clusters exhibiting the EMSTO phenomenon are a general phase in the evolution of massive clusters, one that naturally leads to the particular chemical properties of the ancient GC population. We show that the isolation of EMSTO clusters to intermediate ages is the consequence of observational selection effects. In our proposed scenario, the EMSTO phenomenon is identical to that which establishes the light-element abundance variations that are ubiquitous in the ancient GC population. Our scenario makes a strong prediction: EMSTO clusters will exhibit abundance variations in the light-elements characteristic of the ancient GC population.

  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. Larger red-shift in optical emissions obtained from the thin films of globular proteins (BSA, lysozyme) - polyelectrolyte (PAA) complexes

    NASA Astrophysics Data System (ADS)

    Talukdar, Hrishikesh; Kundu, Sarathi; Basu, Saibal

    2016-09-01

    Globular proteins (lysozyme and BSA) and polyelectrolyte (sodium polyacrylic acid) are used to form protein-polyelectrolyte complexes (PPC). Out-of-plane structures of ≈30-60 nm thick PPC films and their surface morphologies have been studied by using X-ray reflectivity and atomic force microscopy, whereas optical behaviors of PPC and protein conformations have been studied by using UV-vis, photoluminescence and FTIR spectroscopy respectively. Our study reveals that thin films of PPC show a larger red-shift of 23 and 16 nm in the optical emissions in comparison to that of pure protein whereas bulk PPC show a small blue-shift of ≈3 nm. A small amount of peak-shift is found to occur due to the heat treatment or concentration variation of the polyelectrolyte/protein in bulk solution but cannot produce such film thickness independent larger red-shift. Position of the emission peak remains nearly unchanged with the film thickness. Mechanism for such larger red-shift has been proposed.

  6. Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy.

    PubMed

    Li, Conggang; Charlton, Lisa M; Lakkavaram, Asha; Seagle, Christopher; Wang, Guifang; Young, Gregory B; Macdonald, Jeffrey M; Pielak, Gary J

    2008-05-21

    In-cell NMR provides a valuable means to assess how macromolecules, with concentrations up to 300 g/L in the cytoplasm, affect the structure and dynamics of proteins at atomic resolution. Here an intrinsically disordered protein, alpha-synuclein (alphaSN), and a globular protein, chymotrypsin inhibitor 2 (CI2) were examined by using in-cell NMR. High-resolution in-cell spectra of alphaSN can be obtained, but CI2 leaks from the cell and the remaining intracellular CI2 is not detectable. Even after stabilizing the cells from leakage by using alginate encapsulation, no CI2 signal is detected. From in vitro studies we conclude that this difference in detectability is the result of the differential dynamical response of disordered and ordered proteins to the changes of motion caused by the increased viscosity in cells.

  7. 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.

  8. GLOBULAR CLUSTER ABUNDANCES FROM HIGH-RESOLUTION, INTEGRATED-LIGHT SPECTROSCOPY. III. THE LARGE MAGELLANIC CLOUD: Fe AND AGES

    SciTech Connect

    Colucci, Janet E.; Bernstein, Rebecca A.; McWilliam, Andrew E-mail: rab@ucolick.org E-mail: andy@ociw.edu

    2011-07-01

    In this paper, we refine our method for the abundance analysis of high-resolution spectroscopy of the integrated light of unresolved globular clusters (GCs). This method was previously demonstrated for the analysis of old (>10 Gyr) Milky Way (MW) GCs. Here, we extend the technique to young clusters using a training set of nine GCs in the Large Magellanic Cloud. Depending on the signal-to-noise ratio of the data, we use 20-100 Fe lines per cluster to successfully constrain the ages of old clusters to within a {approx}5 Gyr range, the ages of {approx}2 Gyr clusters to a 1-2 Gyr range, and the ages of the youngest clusters (0.05-1 Gyr) to a {approx}200 Myr range. We also demonstrate that we can measure [Fe/H] in clusters with any age less than 12 Gyr with similar or only slightly larger uncertainties (0.1-0.25 dex) than those obtained for old MW GCs (0.1 dex); the slightly larger uncertainties are due to the rapid evolution in stellar populations at these ages. In this paper, we present only Fe abundances and ages. In the next paper in this series, we present our complete analysis of {approx}20 elements for which we are able to measure abundances. For several of the clusters in this sample, there are no high-resolution abundances in the literature from individual member stars; our results are the first detailed chemical abundances available. The spectra used in this paper were obtained at Las Campanas with the echelle on the du Pont Telescope and with the MIKE spectrograph on the Magellan Clay Telescope.

  9. Detailed Abundances for a Large Sample of Giant Stars in the Globular Cluster 47 Tucanae (NGC 104)

    NASA Astrophysics Data System (ADS)

    Cordero, M. J.; Pilachowski, C. A.; Johnson, C. I.; McDonald, I.; Zijlstra, A. A.; Simmerer, J.

    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.

  10. Globular Cluster Abundances from High-resolution, Integrated-light Spectroscopy. III. The Large Magellanic Cloud: Fe and Ages

    NASA Astrophysics Data System (ADS)

    Colucci, Janet E.; Bernstein, Rebecca A.; Cameron, Scott A.; McWilliam, Andrew

    2011-07-01

    In this paper, we refine our method for the abundance analysis of high-resolution spectroscopy of the integrated light of unresolved globular clusters (GCs). This method was previously demonstrated for the analysis of old (>10 Gyr) Milky Way (MW) GCs. Here, we extend the technique to young clusters using a training set of nine GCs in the Large Magellanic Cloud. Depending on the signal-to-noise ratio of the data, we use 20-100 Fe lines per cluster to successfully constrain the ages of old clusters to within a ~5 Gyr range, the ages of ~2 Gyr clusters to a 1-2 Gyr range, and the ages of the youngest clusters (0.05-1 Gyr) to a ~200 Myr range. We also demonstrate that we can measure [Fe/H] in clusters with any age less than 12 Gyr with similar or only slightly larger uncertainties (0.1-0.25 dex) than those obtained for old MW GCs (0.1 dex) the slightly larger uncertainties are due to the rapid evolution in stellar populations at these ages. In this paper, we present only Fe abundances and ages. In the next paper in this series, we present our complete analysis of ~20 elements for which we are able to measure abundances. For several of the clusters in this sample, there are no high-resolution abundances in the literature from individual member stars; our results are the first detailed chemical abundances available. The spectra used in this paper were obtained at Las Campanas with the echelle on the du Pont Telescope and with the MIKE spectrograph on the Magellan Clay Telescope. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  11. 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

  12. 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.

  13. 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.

  14. The RING domain of the scaffold protein Ste5 adopts a molten globular character with high thermal and chemical stability.

    PubMed

    Walczak, Michal J; Samatanga, Brighton; van Drogen, Frank; Peter, Matthias; Jelesarov, Ilian; Wider, Gerhard

    2014-01-27

    Ste5 is a scaffold protein that controls the pheromone response of the MAP-kinase cascade in yeast cells. Upon pheromone stimulation, Ste5 (through its RING-H2 domain) interacts with the β and γ subunits of an activated heterodimeric G protein and promotes activation of the MAP-kinase cascade. With structural and biophysical studies, we show that the Ste5 RING-H2 domain exists as a molten globule under native buffer conditions, in yeast extracts, and even in denaturing conditions containing urea (7 M). Furthermore, it exhibits high thermal stability in native conditions. Binding of the Ste5 RING-H2 domain to the physiological Gβ/γ (Ste4/Ste18) ligand is accompanied by a conformational transition into a better folded, more globular structure. This study reveals novel insights into the folding mechanism and recruitment of binding partners by the Ste5 RING-H2 domain. We speculate that many RING domains may share a similar mechanism of substrate recognition and molten-globule-like character.

  15. The RING domain of the scaffold protein Ste5 adopts a molten globular character with high thermal and chemical stability.

    PubMed

    Walczak, Michal J; Samatanga, Brighton; van Drogen, Frank; Peter, Matthias; Jelesarov, Ilian; Wider, Gerhard

    2014-01-27

    Ste5 is a scaffold protein that controls the pheromone response of the MAP-kinase cascade in yeast cells. Upon pheromone stimulation, Ste5 (through its RING-H2 domain) interacts with the β and γ subunits of an activated heterodimeric G protein and promotes activation of the MAP-kinase cascade. With structural and biophysical studies, we show that the Ste5 RING-H2 domain exists as a molten globule under native buffer conditions, in yeast extracts, and even in denaturing conditions containing urea (7 M). Furthermore, it exhibits high thermal stability in native conditions. Binding of the Ste5 RING-H2 domain to the physiological Gβ/γ (Ste4/Ste18) ligand is accompanied by a conformational transition into a better folded, more globular structure. This study reveals novel insights into the folding mechanism and recruitment of binding partners by the Ste5 RING-H2 domain. We speculate that many RING domains may share a similar mechanism of substrate recognition and molten-globule-like character. PMID:24356903

  16. 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.

  17. 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}ȯ . 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}ȯ . 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}ȯ for the all-cluster stack and \\overline{{M}{{BH}}({{massive}})}\\lt {51,000}\\quad {M}ȯ 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}ȯ . 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.

  18. A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

    NASA Astrophysics Data System (ADS)

    Kolinski, Andrzej; Godzik, Adam; Skolnick, Jeffrey

    1993-05-01

    Starting from amino acid sequence alone, a general approach for simulating folding into the molten globule or rigid, native state depending on sequence is described. In particular, the 3D folds of two simple designed proteins have been predicted using a Monte Carlo folding algorithm. The model employs a very flexible hybrid lattice representation of the protein conformation, and fast lattice dynamics. A full rotamer library for side group conformations, and potentials of mean force of short and long range interactions have been extracted from the statistics of a high resolution set of nonhomologous, 3D structures of globular proteins. The simulated folding process starts from an arbitrary random conformation and relatively rapidly assembles a well defined four helix bundle. The very cooperative folding of the model systems is facilitated by the proper definition of the model protein hydrogen bond network, and multibody interactions of the side groups. The two sequences studied exhibit very different behavior. The first one, in excellent agreement with experiment, folds to a thermodynamically very stable four helix bundle that has all the properties postulated for the molten globule state. The second protein, having a more heterogeneous sequence, at lower temperature undergoes a transition from the molten globule state to the unique native state exhibiting a fixed pattern of side group packing. This marks the first time that the ability to predict a molten globule or a unique native state from sequence alone has been achieved. The implications for the general solution of the protein folding problem are briefly discussed.

  19. Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins.

    PubMed

    Zhou, X Z

    1995-12-01

    The translational friction coefficients and intrinsic viscosities of four proteins (ribonuclease A, lysozyme, myoglobin, and chymotrypsinogen A) are calculated using atomic-level structural details. Inclusion of a 0.9-A-thick hydration shell allows calculated results for both hydrodynamic properties of each protein to reproduce experimental data. The use of detailed protein structures is made possible by relating translational friction and intrinsic viscosity to capacitance and polarizability, which can be calculated easily. The 0.9-A hydration shell corresponds to a hydration level of 0.3-0.4 g water/g protein. Hydration levels within this narrow range are also found by a number of other techniques such as nuclear magnetic resonance spectroscopy, infrared spectroscopy, calorimetry, and computer simulation. The use of detailed protein structures in predicting hydrodynamic properties thus allows hydrodynamic measurement to join the other techniques in leading to a unified picture of protein hydration. In contrast, earlier interpretations of hydrodynamic data based on modeling proteins as ellipsoids gave hydration levels that varied widely from protein to protein and thus challenged the existence of a unified picture of protein hydration. PMID:8599637

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  1. SuperLooper—a prediction server for the modeling of loops in globular and membrane proteins

    PubMed Central

    Hildebrand, Peter W.; Goede, Andrean; Bauer, Raphael A.; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

    2009-01-01

    SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180 000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 Å, for loops up to six residues or <3 Å for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/ PMID:19429894

  2. SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins.

    PubMed

    Hildebrand, Peter W; Goede, Andrean; Bauer, Raphael A; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

    2009-07-01

    SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180,000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 A, for loops up to six residues or <3 A for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/.

  3. 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. PMID:24604128

  4. The Surface-Mediated Unfolding Kinetics of Globular Proteins is Dependent on Molecular Weight and Temperature

    SciTech Connect

    Patananan, Alexander; Goheen, Steven C

    2008-12-01

    The adsorption and unfolding of proteins on rigid surfaces is characterized by numerous chemical and physical interactions such as hydrogen bonds, disulfide bridges, hydrophobic effects, and London forces. The kinetics of unfolding is dependent on pH, temperature, surface chemistry, as well as protein deformability and structure. In practical applications, this fundamental process has broad implications in biomedical engineering (i.e. artificial implants, drug delivery, and surgical equipment), nanotechnology, maritime construction, and chromatography. However, little is known about the mechanisms behind unfolding because of the atomic lengths and rapid time scales associated with the surface-mediated pathway. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the 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 (HPLC). The elution profiles and retention times were obtained by UV/Vis spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to protein unfolding on the non-porous surfaces. This data, and those of previous studies, fit a linear trend between percent unfolding after a fixed (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. 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 confirms

  5. Native topology determines force-induced unfolding pathways in globular proteins

    NASA Astrophysics Data System (ADS)

    Klimov, D. K.; Thirumalai, D.

    2000-06-01

    Single-molecule manipulation techniques reveal that stretching unravels individually folded domains in the muscle protein titin and the extracellular matrix protein tenascin. These elastic proteins contain tandem repeats of folded domains with -sandwich architecture. Herein, we propose by stretching two model sequences (S1 and S2) with four-stranded -barrel topology that unfolding forces and pathways in folded domains can be predicted by using only the structure of the native state. Thermal refolding of S1 and S2 in the absence of force proceeds in an all-or-none fashion. In contrast, phase diagrams in the force-temperature (f,T) plane and steered Langevin dynamics studies of these sequences, which differ in the native registry of the strands, show that S1 unfolds in an allor-none fashion, whereas unfolding of S2 occurs via an obligatory intermediate. Force-induced unfolding is determined by the native topology. After proving that the simulation results for S1 and S2 can be calculated by using native topology alone, we predict the order of unfolding events in Ig domain (Ig27) and two fibronectin III type domains (9FnIII and 10FnIII). The calculated unfolding pathways for these proteins, the location of the transition states, and the pulling speed dependence of the unfolding forces reflect the differences in the way the strands are arranged in the native states. We also predict the mechanisms of force-induced unfolding of the coiled-coil spectrin (a three-helix bundle protein) for all 20 structures deposited in the Protein Data Bank. Our approach suggests a natural way to measure the phase diagram in the (f,C) plane, where C is the concentration of denaturants.

  6. Functionalized self-assembly of gold nanoparticles functionalized with amino acids and aleurone globular protein

    NASA Astrophysics Data System (ADS)

    Tomoaia-Cotisel, Maria; Mocanu, Aurora; Horovitz, Ossi; Indrea, Emil; Tomoaia, Gheorghe; Bratu, Ioan

    2009-01-01

    Gold colloidal aqueous solutions were synthesized and characterized by UV-Vis spectroscopy and TEM. Gold films were prepared on silanized glass slides at room temperature and with thermal treatment. The interaction of gold nanoparticles with biomolecules (amino acids, protein) was studied using UV-Vis spectroscopy, AFM, TEM and X-ray diffraction.

  7. 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. PMID:26320075

  8. Why Do Tetrapropylammonium Chloride and Sulphate Salts Destabilize the Native State of Globular Proteins?

    PubMed Central

    2014-01-01

    It has recently been shown that aqueous solutions of tetrapropylammonium chloride and sulphate salts destabilize the folded conformation of Trp-peptides (Dempsey et al., 2011). This result is rationalized by the application of a statistical thermodynamic approach (Graziano, 2010). It is shown that the magnitude of the solvent-excluded volume effect, the main contribution for the native state stability, decreases in both aqueous 2 M TPACl solution and aqueous 1 M TPA2SO4 solution. This happens because TPA+ ions are so large in size and interact so weakly with water molecules, due to their very low charge density, to be able to counteract the electrostrictive effect of chloride and sulphate ions on the water structure, so that the density of their aqueous solutions is smaller or only slightly larger than that of water. PMID:24616650

  9. 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; 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 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

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

    PubMed

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

    2015-07-01

    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. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.

  11. 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.

  12. 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

  13. A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

    PubMed

    Tsai, Cheng-Fang; Lee, Kuei-Jen

    2011-01-01

    In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (δ). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the proteins is represented by the mean radius of gyration (R(g) ), which follows the Flory scaling law, R(g) ∝ N(ν). The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, |q(i)| ≥ 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range.

  14. 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

  15. Crystallization and preliminary X-ray crystallographic analysis of an artificial molten-globular-like triosephosphate isomerase protein of mixed phylogenetic origin

    PubMed Central

    Goyal, Venuka Durani; Yadav, Pooja; Kumar, Ashwani; Ghosh, Biplab; Makde, Ravindra D.

    2014-01-01

    A bioinformatics-based protein-engineering approach called consensus design led to the construction of a chimeric triosephosphate isomerase (TIM) protein called ccTIM (curated consensus TIM) which is as active as Saccharomyces cerevisiae TIM despite sharing only 58% sequence identity with it. The amino-acid sequence of this novel protein is as identical to native sequences from eukaryotes as to those from prokaryotes and shares some biophysical traits with a molten globular protein. Solving its crystal structure would help in understanding the physical implications of its bioinformatics-based sequence. In this report, the ccTIM protein was successfully crystallized using the microbatch-under-oil method and a full X-ray diffraction data set was collected to 2.2 Å resolution using a synchrotron-radiation source. The crystals belonged to space group C2221, with unit-cell parameters a = 107.97, b = 187.21, c = 288.22 Å. Matthews coefficient calculations indicated the presence of six dimers in the asymmetric unit, with an approximate solvent content of 46.2%. PMID:25372821

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Binary Stars in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Mateo, M.; Murdin, P.

    2000-11-01

    Globular clusters have long been known to be among the richest stellar groupings within our Galaxy, but for many years they were believed to be largely devoid of the most minimal stellar group: binary stars (see BINARY STARS: OVERVIEW). For many years, the only evidence that any binaries existed in these clusters came from the presence of BLUE STRAGGLERS—stars that appear to be significantly you...

  1. 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.

  2. GLOBULAR CLUSTER ABUNDANCES FROM HIGH-RESOLUTION, INTEGRATED-LIGHT SPECTROSCOPY. IV. THE LARGE MAGELLANIC CLOUD: {alpha}, Fe-PEAK, LIGHT, AND HEAVY ELEMENTS

    SciTech Connect

    Colucci, Janet E.; Bernstein, Rebecca A.; McWilliam, Andrew E-mail: rab@ucolick.org E-mail: andy@ociw.edu

    2012-02-10

    We present detailed chemical abundances in eight clusters in the Large Magellanic Cloud (LMC). We measure abundances of 22 elements for clusters spanning a range in age of 0.05-12 Gyr, providing a comprehensive picture of the chemical enrichment and star formation history of the LMC. The abundances were obtained from individual absorption lines using a new method for analysis of high-resolution (R {approx} 25,000), integrated-light (IL) spectra of star clusters. This method was developed and presented in Papers I, II, and III of this series. In this paper, we develop an additional IL {chi}{sup 2}-minimization spectral synthesis technique to facilitate measurement of weak ({approx}15 mA) spectral lines and abundances in low signal-to-noise ratio data (S/N {approx} 30). Additionally, we supplement the IL abundance measurements with detailed abundances that we measure for individual stars in the youngest clusters (age < 2 Gyr) in our sample. In both the IL and stellar abundances we find evolution of [{alpha}/Fe] with [Fe/H] and age. Fe-peak abundance ratios are similar to those in the Milky Way (MW), with the exception of [Cu/Fe] and [Mn/Fe], which are sub-solar at high metallicities. The heavy elements Ba, La, Nd, Sm, and Eu are significantly enhanced in the youngest clusters. Also, the heavy to light s-process ratio is elevated relative to the MW ([Ba/Y] >+0.5) and increases with decreasing age, indicating a strong contribution of low-metallicity asymptotic giant branch star ejecta to the interstellar medium throughout the later history of the LMC. We also find a correlation of IL Na and Al abundances with cluster mass in the sense that more massive, older clusters are enriched in the light elements Na and Al with respect to Fe, which implies that these clusters harbor star-to-star abundance variations as is common in the MW. Lower mass, intermediate-age, and young clusters have Na and Al abundances that are lower and more consistent with LMC field stars. Our

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

    PubMed Central

    2009-01-01

    Background 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. Results 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 Å) 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. Conclusion 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. PMID:20038291

  4. 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

  5. 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. PMID:15802651

  6. 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.

  7. Novae in globular clusters

    SciTech Connect

    Kato, Mariko; Hachisu, Izumi; Henze, Martin

    2013-12-10

    We present the first light-curve analysis of Population II novae that appeared in M31 globular clusters. Our light-curve models, based on the optically thick wind theory, reproduce well both the X-ray turn-on and turnoff times with the white dwarf (WD) mass of about 1.2 M {sub ☉} for M31N 2007-06b in Bol 111 and about 1.37 M {sub ☉} for M31N 2010-10f in Bol 126. The transient supersoft X-ray source CXO J004345 in Bol 194 is highly likely a nova remnant of 1.2-1.3 M {sub ☉} WD. These WD masses are quite consistent with the temperatures deduced from X-ray spectra. We also present the dependence of nova light curves on the metallicity in the range from [Fe/H] = 0.4 to –2.7. Whereas strong optically thick winds are accelerated in Galactic disk novae owing to a large Fe opacity peak, only weak winds occur in Population II novae with low Fe abundance. Thus, nova light curves are systematically slow in low Fe environment. For an extremely low Fe abundance normal nova outbursts may not occur unless the WD is very massive. We encourage V or y filter observation rather than R as well as high cadence X-ray monitorings to open quantitative studies of extragalactic novae.

  8. Modelling the Distribution of Globular Cluster Masses

    NASA Astrophysics Data System (ADS)

    McLaughlin, Dean E.; Pudritz, Ralph E.

    1994-12-01

    On the basis of various observational evidence, we argue that the overall present-day distribution of mass in globular cluster systems around galaxies as diverse as M87 and the Milky Way may be in large part reflective of robust formation processes, and little influenced by subsequent dynamical evolution of the globulars. With this in mind, Harris & Pudritz (1994, ApJ, 429, 177) have recently suggested that globular clusters with a range of masses are formed in pregalactic ``supergiant molecular clouds'' which grow by (coalescent) binary collisions with other clouds. We develop this idea more fully by solving for the steady-state mass distributions resulting from such coalescent encounters, with provisions made for the disruption of high-mass clouds due to star formation. Agglomeration models have been proposed in various guises to explain the mass spectra of planetesimals, stars, giant molecular clouds and their cores, and galaxies. The present theory generalizes aspects of these models, and appears able to account for the distribution of globular cluster masses at least above the so-called ``turnover'' of the globular cluster luminosity function.

  9. 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

  10. 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.

  11. An instrument for time resolved monitoring of fast chemical transitions: Application to the kinetics of refolding of a globular protein

    NASA Astrophysics Data System (ADS)

    Ratner, Vladimir; Haas, Elisha

    1998-05-01

    The dynamics of kinetic intermediates of protein folding can be studied by time resolved measurements of nonradiative excitation energy transfer, in site-specific labeled protein derivatives, combined with fast mixing experiments. A new device based on the single pulse approach was developed. This experiment is performed over two time scales: the "chemical time scale" of the conformational changes (milliseconds), defined by the rates of changes of conformations in the sample, and the "spectroscopic time scale" (nanoseconds) defined by the lifetimes of the excited states of the fluorescent probes. The chemical process was synchronized by means of a fast mixing stopped flow device. The low cost laser used here is suitable for use with dyes with excitation wavelengths of 337 nm and higher. Up to 20 fluorescence decay curves per second, can be measured within a single stopped flow run. Each fluorescence decay curve is recorded within 250 ns or more. The time resolution (of the spectroscopic time scale) was 0.5 ns. The noise level is low enough to estimate distance distributions from energy transfer experiments, provided that the shortest changeable lifetime component of the fluorescence decay of the donor probes would not be lower than ˜4 ns. The amount of double labeled protein which should be used for each experiment in order to obtain a full data set, with time resolution of 10 ms during protein transition, is only fourfold more than the amount needed for a stopped flow study with steady state fluorescence monitoring. The results obtained for refolding of α-lactalbumin in the presence of 1,8-anilino-naphthalene sulfonic acid from the GuHCl induced denatured state, support the model in which the probe has two states. The first state, is characterized by a fluorescence lifetime of 14.2±0.5 ns and the second by a fluorescence lifetime of 0.5±0.4 ns or less. During refolding the dye is transferred from the first state to the second, at a rate that coincides with the

  12. 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.

  13. 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

  14. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.

    PubMed

    Fernandez-Fuentes, Narcis; Querol, Enrique; Aviles, Francesc X; Sternberg, Michael J E; Oliva, Baldomero

    2005-09-01

    In protein structure prediction, a central problem is defining the structure of a loop connecting 2 secondary structures. This problem frequently occurs in homology modeling, fold recognition, and in several strategies in ab initio structure prediction. In our previous work, we developed a classification database of structural motifs, ArchDB. The database contains 12,665 clustered loops in 451 structural classes with information about phi-psi angles in the loops and 1492 structural subclasses with the relative locations of the bracing secondary structures. Here we evaluate the extent to which sequence information in the loop database can be used to predict loop structure. Two sequence profiles were used, a HMM profile and a PSSM derived from PSI-BLAST. A jack-knife test was made removing homologous loops using SCOP superfamily definition and predicting afterwards against recalculated profiles that only take into account the sequence information. Two scenarios were considered: (1) prediction of structural class with application in comparative modeling and (2) prediction of structural subclass with application in fold recognition and ab initio. For the first scenario, structural class prediction was made directly over loops with X-ray secondary structure assignment, and if we consider the top 20 classes out of 451 possible classes, the best accuracy of prediction is 78.5%. In the second scenario, structural subclass prediction was made over loops using PSI-PRED (Jones, J Mol Biol 1999;292:195-202) secondary structure prediction to define loop boundaries, and if we take into account the top 20 subclasses out of 1492, the best accuracy is 46.7%. Accuracy of loop prediction was also evaluated by means of RMSD calculations. PMID:16021623

  15. 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.

  16. Globular cluster ages

    PubMed Central

    Jimenez, Raul

    1998-01-01

    We review two new methods to determine the age of globular clusters (GCs). These two methods are more accurate than the classical isochrone fitting technique. The first method is based on the morphology of the horizontal branch and is independent of the distance modulus of the globular cluster. The second method uses a careful binning of the stellar luminosity function and determines simultaneously the distance and age of the GC. We find that the oldest galactic GCs have an age of 13.5 ± 2 gigayears (Gyr). The absolute minimum age for the oldest GCs is 10.5 Gyr (with 99% confidence) and the maximum 16.0 Gyr (with 99% confidence). Therefore, an Einstein–De Sitter Universe (Ω = 1) is not totally ruled out if the Hubble constant is about 65 ± 10 Km s−1 Mpc−1. PMID:9419317

  17. 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.

  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. 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.

  20. A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.

    PubMed

    Hall, Damien; Li, Songling; Yamashita, Kazuo; Azuma, Ryuzo; Carver, John A; Standley, Daron M

    2014-06-01

    We present a novel protein distance matrix based on the minimum line of arc between two points on the surface of a protein. Two methods for calculating this distance matrix are developed and contrasted. The first method, which we have called TOPOL, is an approximate rule based algorithm consisting of successive rounds of vector addition. The second method is adapted from the graph theoretic approach of Dijkstra. Both procedures are demonstrated using cytochrome c, a 12,500 Da protein, as a test case. In respect to computational speed and accuracy the TOPOL procedure compares favorably against the more complex method based on shortest path enumeration over a surface manifold grid. Some potential uses of the algorithmic approaches and calculated surface protein distance measurement are discussed. PMID:24589301

  1. 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. PMID:25330023

  2. Super-Resolution Fluorescence of Huntingtin Reveals Growth of Globular Species into Short Fibers and Coexistence of Distinct Aggregates

    PubMed Central

    2015-01-01

    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. PMID:25330023

  3. 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

  4. Microlensing in Globular Clusters: the First Confirmed Lens

    NASA Astrophysics Data System (ADS)

    Jetzer, Philippe

    2015-01-01

    Microlensing observations toward globular clusters could be very useful to probe their low mass star and brown dwarf content. Using the large set of microlensing events detected so far toward the Galactic centre we investigated whether for some of the observed events the lenses are located in the Galactic globular clusters. Indeed, we found that in four cases some events might be due to lenses located in the globular clusters themselves. Moreover, we discuss a microlensing event found in M22. Using the adaptive optics system NACO at ESO VLT it was possible to identify the lens, which turned out to be a low mass star of about 0.18 solar masses in the globular cluster M22 itself.

  5. Large-scale identification of yeast integral membrane protein interactions

    PubMed Central

    Miller, John P.; Lo, Russell S.; Ben-Hur, Asa; Desmarais, Cynthia; Stagljar, Igor; Noble, William Stafford; Fields, Stanley

    2005-01-01

    We carried out a large-scale screen to identify interactions between integral membrane proteins of Saccharomyces cerevisiae by using a modified split-ubiquitin technique. Among 705 proteins annotated as integral membrane, we identified 1,985 putative interactions involving 536 proteins. To ascribe confidence levels to the interactions, we used a support vector machine algorithm to classify interactions based on the assay results and protein data derived from the literature. Previously identified and computationally supported interactions were used to train the support vector machine, which identified 131 interactions of highest confidence, 209 of the next highest confidence, 468 of the next highest, and the remaining 1,085 of low confidence. This study provides numerous putative interactions among a class of proteins that have been difficult to analyze on a high-throughput basis by other approaches. The results identify potential previously undescribed components of established biological processes and roles for integral membrane proteins of ascribed functions. PMID:16093310

  6. 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.

  7. 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.

  8. 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.

  9. 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)

  10. Parkes Observations of Globular Cluster Pulsars

    NASA Astrophysics Data System (ADS)

    Bailes, M.; Zhu, J.; Richter, S.

    2005-07-01

    Follow-up observations of pulsars from the Swinburne intermediate latitude survey with the Parkes radio telescope have caused us to question the association of PSR B1718-19 with the globular cluster NGC 6342 given the proximity of PSR J1721-1939 to the cluster. We have also found that the millisecond pulsar near the core of NGC 6624 has a large period second derivative, which would change the sign of the first derivative in about 6000 years. This is consistent with the pulsar experiencing a large gravitational perturbation from the cluster core.

  11. 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.

  12. 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.

  13. ROTATING GLOBULAR CLUSTERS

    SciTech Connect

    Bianchini, P.; Varri, A. L.; Bertin, G.; Zocchi, A.

    2013-07-20

    Internal rotation is thought to play a major role in the dynamics of some globular clusters. However, in only a few cases has internal rotation been studied by the quantitative application of realistic and physically justified global models. Here, we present a dynamical analysis of the photometry and three-dimensional kinematics of {omega} Cen, 47 Tuc, and M15, by means of a recently introduced family of self-consistent axisymmetric rotating models. The three clusters, characterized by different relaxation conditions, show evidence of differential rotation and deviations from sphericity. The combination of line-of-sight velocities and proper motions allows us to determine their internal dynamics, predict their morphology, and estimate their dynamical distance. The well-relaxed cluster 47 Tuc is interpreted very well by our model; internal rotation is found to explain the observed morphology. For M15, we provide a global model in good agreement with the data, including the central behavior of the rotation profile and the shape of the ellipticity profile. For the partially relaxed cluster {omega} Cen, the selected model reproduces the complex three-dimensional kinematics; in particular, the observed anisotropy profile, characterized by a transition from isotropy to weakly radial anisotropy and then to tangential anisotropy in the outer parts. The discrepancy found for the steep central gradient in the observed line-of-sight velocity dispersion profile and for the ellipticity profile is ascribed to the condition of only partial relaxation of this cluster and the interplay between rotation and radial anisotropy.

  14. 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.

  15. 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.

  16. Variable Stars in the Large Magellanic Cloud Globular Cluster NGC 2257. I. Results Based on 2007-2008 B, V Photometry

    NASA Astrophysics Data System (ADS)

    Nemec, James M.; Walker, Alistair; Jeon, Young-Beom

    2009-11-01

    The variable stars in the Large Magellanic Cloud star cluster NGC 2257 are reinvestigated using photometry (to ~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 ~0.36 day and period ratios P 1/P 0 ~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.

  17. 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.

  18. 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.

  19. 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.

  20. Globular Clusters and the Milky Way Connected by Chemistry

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    There are two ways to study galaxy formation and evolution: one is to observe a large number of galaxies at a variety of redshifts, the other is to observe in detail just a few nearby galaxies. The precision achievable by the latter method enables the galactic history, including the formation and early evolution, to be studied. Globular clusters provide targets for the second method. We show how the chemical content of Milky Way globular clusters can be used to place them on a timeline charting the history of our Galaxy. The results suggest that different α-elements trace different processes of Milky Way chemical evolution.

  1. Large scale protein separations: engineering aspects of chromatography.

    PubMed

    Chisti, Y; Moo-Young, M

    1990-01-01

    The engineering considerations common to large scale chromatographic purification of proteins are reviewed. A discussion of the industrial chromatography fundamentals is followed by aspects which affect the scale of separation. The separation column geometry, the effect of the main operational parameters on separation performance, and the physical characteristics of column packing are treated. Throughout, the emphasis is on ion exchange and size exclusion techniques which together constitute the major portion of commercial chromatographic protein purifications. In all cases, the state of current technology is examined and areas in need of further development are noted. The physico-chemical advances now underway in chromatographic separation of biopolymers would ensure a substantially enhanced role for these techniques in industrial production of products of new biotechnology.

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

    DOE PAGES

    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 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

  3. 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.

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

    PubMed

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

    2015-04-01

    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.

  5. Folding of a large protein at high structural resolution

    PubMed Central

    Walters, Benjamin T.; Mayne, Leland; Hinshaw, James R.; Sosnick, Tobin R.; Englander, S. Walter

    2013-01-01

    Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (∼100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways. PMID:24191053

  6. 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

  7. 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.

  8. Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

    SciTech Connect

    Nigsch, Florian; Mitchell, John B.O.

    2008-09-01

    The combination of models for protein target prediction with large databases containing toxicological information for individual molecules allows the derivation of 'toxiclogical' profiles, i.e., to what extent are molecules of known toxicity predicted to interact with a set of protein targets. To predict protein targets of drug-like and toxic molecules, we built a computational multiclass model using the Winnow algorithm based on a dataset of protein targets derived from the MDL Drug Data Report. A 15-fold Monte Carlo cross-validation using 50% of each class for training, and the remaining 50% for testing, provided an assessment of the accuracy of that model. We retained the 3 top-ranking predictions and found that in 82% of all cases the correct target was predicted within these three predictions. The first prediction was the correct one in almost 70% of cases. A model built on the whole protein target dataset was then used to predict the protein targets for 150 000 molecules from the MDL Toxicity Database. We analysed the frequency of the predictions across the panel of protein targets for experimentally determined toxicity classes of all molecules. This allowed us to identify clusters of proteins related by their toxicological profiles, as well as toxicities that are related. Literature-based evidence is provided for some specific clusters to show the relevance of the relationships identified.

  9. Hot subdwarfs in globular clusters

    SciTech Connect

    Drukier, G.A.; Fahlman, G.G.; Richter, H.B. )

    1989-07-01

    Spectra of faint blue stars in the globular clusters M71 and M4 are presented. The spectra suggest that they are hot subdwarfs. Arguments in favor of membership in their respective clusters and comments regarding their evolutionary status are given. 18 refs.

  10. Carbon and nitrogen abundance variations in globular cluster red giants

    NASA Astrophysics Data System (ADS)

    Martell, Sarah L.

    2008-06-01

    This dissertation describes investigations into two of the persistent questions of elemental abundances in Galactic globular clusters: the phenomenon of deep mixing, observed through the progressive depletion of surface carbon abundance as stars evolve along the red giant branch, and abundance bimodality, a phenomenon observed only in globular clusters, in which a subset of stars in a given globular cluster have a distinctive pattern of elemental enhancements and depletions relative to the Solar pattern. The first chapter gives an introduction to the history of globular cluster abundance studies, with particular focus on low-resolution spectroscopy. For both deep mixing and abundance bimodality, the leading theoretical models and the data which support and challenge them are laid out. Each section ends with a description of presently-unanswered questions; these are the motivation for the various projects contained in this dissertation. The second chapter describes the use of molecular handstrengths for determining elemental abundances from low-resolution spectra, and introduces a new CH bandstrength index that is designed to be sensitive to carbon abundance and insensitive to nitrogen abundance in Pop. II red giants over a wide range of metallicity. Various CH indices defined elsewhere in the literature are also discussed, and are shown to have comparable accuracy to the new index only over a limited range of stellar properties. Carbon abundances determined using the new CH index are compared to literature abundances for a few stars, and general concordance with published abundances is found. The third chapter contains a large-scale application of the new CH index: a survey of present-day carbon abundances and calculated carbon depletion rates in bright red giants belonging to eleven Galactic globular clusters spanning the full metallicity range of halo globular clusters. Targets were selected with similar evolutionary states, were observed with one instrument on

  11. 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.

  12. 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.

  13. 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.

  14. 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. PMID:27500308

  15. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins

    PubMed Central

    Adachi, Jun; Kumar, Chanchal; Zhang, Yanling; Olsen, Jesper V; Mann, Matthias

    2006-01-01

    Background Urine is a desirable material for the diagnosis and classification of diseases because of the convenience of its collection in large amounts; however, all of the urinary proteome catalogs currently being generated have limitations in their depth and confidence of identification. Our laboratory has developed methods for the in-depth characterization of body fluids; these involve a linear ion trap-Fourier transform (LTQ-FT) and a linear ion trap-orbitrap (LTQ-Orbitrap) mass spectrometer. Here we applied these methods to the analysis of the human urinary proteome. Results We employed one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis and reverse phase high-performance liquid chromatography for protein separation and fractionation. Fractionated proteins were digested in-gel or in-solution, and digests were analyzed with the LTQ-FT and LTQ-Orbitrap at parts per million accuracy and with two consecutive stages of mass spectrometric fragmentation. We identified 1543 proteins in urine obtained from ten healthy donors, while essentially eliminating false-positive identifications. Surprisingly, nearly half of the annotated proteins were membrane proteins according to Gene Ontology (GO) analysis. Furthermore, extracellular, lysosomal, and plasma membrane proteins were enriched in the urine compared with all GO entries. Plasma membrane proteins are probably present in urine by secretion in exosomes. Conclusion Our analysis provides a high-confidence set of proteins present in human urinary proteome and provides a useful reference for comparing datasets obtained using different methodologies. The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future. PMID:16948836

  16. 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

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

    PubMed

    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

  18. 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.

  19. Origin and evolution of yolk proteins: expansion and functional diversification of large lipid transfer protein superfamily.

    PubMed

    Wu, Long Tao; Hui, Jerome H L; Chu, Ka Hou

    2013-04-01

    Vitellogenin (VTG) and apolipoprotein (APO) play a central role in animal reproduction and lipid circulation, respectively. Although previous studies have examined the structural and functional relationships of these large lipid transfer proteins (LLTPs) from an evolutionary perspective, the mechanism in generating these different families have not been addressed in invertebrates. In this study, the most comprehensive phylogenetic and genomic analysis of the LLTP superfamily genes is carried out. We propose the expansion and diversification of LLTPs in invertebrates are mediated via retrotransposon-mediated duplications, followed by either subfunctionalization or neofunctionalization in different lineages. In agreement with a previous hypothesis, our analysis suggests that all LLTPs originate from a series of duplications of a primitive yolk protein gene similar to VTG. Two early consecutive duplications of the yolk protein genes resulted in the formation of microsomal triglyceride transfer protein (MTP) and the APO gene ancestor. Gains and losses of domains and genes occurred in each of these families in different animal lineages, with MTP becoming truncated. MTP maintained only the components stabilizing the huge lipoprotein particle. Surprisingly, for the first time, two VTG-like protein families were found to independently arise in the lineages of insects. This work consolidates the reconstruction of the evolutionary roadmap of the LLTP superfamily and provides the first mechanistic explanation on the expansion of family members via retrotransposition in invertebrates. PMID:23426435

  20. 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.

  1. Extra-Large G Proteins Expand the Repertoire of Subunits in Arabidopsis Heterotrimeric G Protein Signaling.

    PubMed

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

    2015-09-01

    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.

  2. 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.

  3. Large-scale proteomic analysis of membrane proteins.

    PubMed

    Ahram, Mamoun; Springer, David L

    2004-10-01

    Proteomic analysis of membrane proteins is a promising approach for the identification of novel drug targets and/or disease biomarkers. Despite notable technological developments, obstacles related to extraction and solublization of membrane proteins are 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. Frequently, unknown proteins are 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 the presence of transmembrane domains. This review also presents 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Ages of globular clusters and helium diffusion

    NASA Technical Reports Server (NTRS)

    Chaboyer, Brian; Sarajedini, Ata; Demarque, Pierre

    1992-01-01

    Evolutionary tracks have been calculated with alpha-enhanced compositions which cover the entire globular cluster metallicity range and have constructed isochrones which include the effects of microscopic diffusion of helium. The turnoff magnitudes from the isochrones were combined with the theoretical RR Lyrae magnitudes from Lee to determine the ages of 32 Galactic globular clusters using the magnitude difference between the turnoff and horizontal branch. It is found that including the effects of helium diffusion has a negligible effect on the derived ages of globular clusters. Regardless of the inclusion of helium diffusion, a significant age spread of 5 Gyr among the globular clusters is found. The oldest globular clusters studied here are 17 +/- 2 Gyr old.

  11. 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

  12. Recent advances in large-scale protein interactome mapping

    PubMed Central

    Mehta, Virja; Trinkle-Mulcahy, Laura

    2016-01-01

    Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other ‘omics’ data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases. PMID:27158474

  13. The ultraviolet spectra of M31 globular clusters

    NASA Technical Reports Server (NTRS)

    Cowley, A. P.; Burstein, D.

    1988-01-01

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

  14. 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.

  15. Extragalactic Globular Clusters: Tracers of Galaxy Evolution

    NASA Astrophysics Data System (ADS)

    Bassino, Lilia P.

    2008-09-01

    The study of globular cluster systems provides clues about different topics related to galaxy evolution. In the past years we have been investigating the globular cluster systems of galaxies in the Fornax and Antlia clusters, particularly those associated to the cluster-dominant galaxies. We present here the main results related to these systems. All of them have bimodal color distributions, even those around low-luminosity galaxies, that correspond to the metal-poor (``blue'') and metal-rich (``red'') globular cluster subpopulations. The radial and azimuthal projected areal distributions of the globular clusters are also analyzed. Total globular cluster populations are estimated through the luminosity functions. We stress on the properties of the globular cluster systems that allow us to trace possible interaction processes between the galaxies, like tidal stripping of globular clusters. The observational material consists of CCD images obtained with the wide-field MOSAIC Imager of the CTIO 4-m telescope (La Serena, Chile), and the FORS1 camera at the VLT ``Antu'' 8-m telescope (Cerro Paranal, Chile).

  16. 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…

  17. Galactic Globular Cluster Relative Ages

    NASA Astrophysics Data System (ADS)

    De Angeli, Francesca; Piotto, Giampaolo; Cassisi, Santi; Busso, Giorgia; Recio-Blanco, Alejandra; Salaris, Maurizio; Aparicio, Antonio; Rosenberg, Alfred

    2005-07-01

    We present accurate relative ages for a sample of 55 Galactic globular clusters. The ages have been obtained by measuring the difference between the horizontal branch and the turnoff in two internally photometrically homogeneous databases. The mutual consistency of the two data sets has been assessed by comparing the ages of 16 globular clusters in common between the two databases. We have also investigated the consistency of our relative age determination within the recent stellar model framework. All clusters with [Fe/H]<-1.7 are found to be old and coeval, with the possible exception of two objects, which are marginally younger. The age dispersion for the metal-poor clusters is 0.6 Gyr (rms), consistent with a null age dispersion. Intermediate-metallicity clusters (-1.7<[Fe/H]<-0.8) are on average 1.5 Gyr younger than the metal-poor ones, with an age dispersion of 1.0 Gyr (rms) and a total age range of ~3 Gyr. About 15% of the intermediate-metallicity clusters are coeval with the oldest clusters. All the clusters with [Fe/H]>-0.8 are ~1 Gyr younger than the most metal-poor ones, with a relatively small age dispersion, although the metal-rich sample is still too small to allow firmer conclusions. There is no correlation of the cluster age with the galactocentric distance. We briefly discuss the implication of these observational results for the formation history of the Galaxy. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555, and on observations made at the European Southern Observatory, La Silla, Chile, and with the Isaac Newton Group Telescopes.

  18. 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.

  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. A Deep Galex Color-Magnitude Diagram of the Galactic Globular Cluster M79

    NASA Astrophysics Data System (ADS)

    Schiavon, R.; O'Connell, R. W.; Rood, R. T.; Valenti, E.; Ferraro, F.; Green, E.; Liebert, J.; Peterson, R.

    2005-12-01

    Based on deep UV imaging of M 79 (NGC 1904), we have constructed the first GALEX color-magnitude diagram of a Galactic globular cluster. Our photometry reaches three magnitudes deeper in the far-UV than the deepest previous exposures, from the UIT telescope. As a result, we obtain a thorough characterization of the hot population in this well-known globular cluster. Here we present our first results for hot horizontal branch and blue straggler stars. In particular, with the large field of view provided by GALEX we were able to unveil the existence of a very large population of blue straggler candidates at very large distances from the cluster center. This result is discussed in light of the competing scenarios for the formation of blue stragglers in globular clusters. This work was supported in part by GALEX grant NNG05GE50G administered by JPL.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Close binary stars in globular clusters

    NASA Technical Reports Server (NTRS)

    Margon, Bruce

    1991-01-01

    Although close binary stars are thought theoretically to play a major role in globular cluster dynamics, virtually no non-degenerate close binaries are known in clusters. We review the status of observations in this area, and report on two new programs which are finally yielding candidate systems suitable for further study. One of the objects, a close eclipsing system in omega Cen, is also a big straggler, thus finally proving firm evidence that globular cluster blue stragglers really are binary stars.

  6. Globular clusters in the far-ultraviolet: evidence for He-enriched second populations in extra-galactic globular clusters?

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    We investigate the integrated far-ultraviolet (FUV) emission from globular clusters. We present new FUV photometry of M 87's clusters based on archival HST WFPC2 F170W observations. We use these data to test the reliability of published photometry based on HST STIS 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, M 31, M 81 and M 87 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 M 31, M 81 and M 87 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 M 31, M 81 and M 87 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 extra-galactic globular clusters.

  7. Binary Black Holes produced in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Rodriguez, Carl; Morscher, Meagan; Pattabiraman, Bharath; Chatterjee, Sourav; Rasio, Fred

    2015-04-01

    The mergers of binary black holes will be one of the most promising sources for gravitational-wave astronomy; however, the number of sources expected to form dynamically within the dense environments of globular clusters is highly uncertain. We use a Monte Carlo technique to explore the stellar dynamics of globular clusters. This approach can model systems with ~106 stars and realistic stellar physics, enabling the study of even the most massive of galactic globular clusters. We have produced a collection of globular cluster models with structural properties similar to those observed in the Milky Way. We explore the population of binary black holes produced in these models, including the distribution of masses, semi-major axes, and eccentricities. We find that a typical Milky Way globular cluster can produce hundreds of black hole binaries, several tens of which will coalesce within one Hubble time. We use these models to simulate the globular cluster population of a single Milky Way-equivalent galaxy, providing us with the first realistic merger rate of dynamically formed binary black holes in the local universe.

  8. SVM ensemble based transfer learning for large-scale membrane proteins discrimination.

    PubMed

    Mei, Suyu

    2014-01-01

    Membrane proteins play important roles in molecular trans-membrane transport, ligand-receptor recognition, cell-cell interaction, enzyme catalysis, host immune defense response and infectious disease pathways. Up to present, discriminating membrane proteins remains a challenging problem from the viewpoints of biological experimental determination and computational modeling. This work presents SVM ensemble based transfer learning model for membrane proteins discrimination (SVM-TLM). To reduce the data constraints on computational modeling, this method investigates the effectiveness of transferring the homolog knowledge to the target membrane proteins under the framework of probability weighted ensemble learning. As compared to multiple kernel learning based transfer learning model, the method takes the advantages of sparseness based SVM optimization on large data, thus more computationally efficient for large protein data analysis. The experiments on large membrane protein benchmark dataset show that SVM-TLM achieves significantly better cross validation performance than the baseline model.

  9. Computational large-scale mapping of protein-protein interactions using structural complexes.

    PubMed

    Shoemaker, Benjamin; Wuchty, Stefan; Panchenko, Anna R

    2013-01-01

    Although the identification of protein interactions by high-throughput methods progresses at a fast pace, "interactome" datasets still suffer from high rates of false positives and low coverage. To map the interactome of any organism, this unit presents a computational framework to predict protein-protein or gene-gene interactions utilizing experimentally determined evidence of structural complexes, atomic details of binding interfaces and evolutionary conservation.

  10. Rapid, large-scale purification and characterization of 'Ada protein' (O6 methylguanine-DNA methyltransferase) of E. coli.

    PubMed Central

    Bhattacharyya, D; Tano, K; Bunick, G J; Uberbacher, E C; Behnke, W D; Mitra, S

    1988-01-01

    The E. coli Ada protein (O6-methylguanine-DNA methyltransferase) has been purified using a high-level expression vector with a yield of about 3 mg per liter of E. coli culture. The 39-kDa protein has an extinction coefficient (E280 nm (1%)) of 5.3. Its isoelectric point of 7.1 is lower than that predicted from the amino acid content. The homogeneous Ada protein is fully active as a methyl acceptor from O6-methylguanine in DNA. Its reaction with O6-methylguanine in a synthetic DNA has a second-order rate constant of 1.1 x 10(9) M-1 min-1 at O degree C. Both the native form and the protein methylated at Cys-69 are monomeric. The CD spectrum suggests a low alpha-helical content and the radius of gyration of 23 A indicates a compact, globular shape. The middle region of the protein is sensitive to a variety of proteases, including an endogenous activity in E. coli, suggesting that the protein is composed of N-terminal and C-terminal domains connected by a hinge region. E. coli B has a higher level of this protease than does K12. Images PMID:3041376

  11. 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

  12. 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.

  13. A Method for Solution NMR Structural Studies of Large Integral Membrane Proteins: Reverse Micelle Encapsulation

    PubMed Central

    Kielec, Joseph M.; Valentine, Kathleen G.; Wand, A. Joshua

    2009-01-01

    The structural study of membrane proteins perhaps represents one of the greatest challenges of the post-genomic era. While membrane proteins comprise over 50% of current and potential drug targets, their structural characterization lags far behind that of soluble proteins. Nuclear magnetic resonance (NMR) offers great potential not only with respect to structural characterization of integral membrane proteins but may also provide the ability to study the details of small ligand interactions. However, the size limitations of solution NMR have restricted comprehensive structural characterization of membrane protein NMR structures to the relatively small β-barrel proteins or helical proteins of relatively simple topology. In an effort to escape the barriers presented by slow molecular reorientation of large integral membrane proteins solubilized by detergent micelles in water, we have adapted the reverse micelle encapsulation strategy originally developed for the study of large soluble proteins by solution NMR methods. Here we review a novel approach to the solubilization of large integral membrane proteins in reverse micelle surfactants dissolved in low viscosity alkane solvents. The procedure is illustrated with a 54 kDa construct of the homotetrameric KcsA potassium channel. PMID:19665988

  14. Core-Cone Structured Monodispersed Mesoporous Silica Nanoparticles with Ultra-large Cavity for Protein Delivery.

    PubMed

    Xu, Chun; Yu, Meihua; Noonan, Owen; Zhang, Jun; Song, Hao; Zhang, Hongwei; Lei, Chang; Niu, Yuting; Huang, Xiaodan; Yang, Yannan; Yu, Chengzhong

    2015-11-25

    A new type of monodispersed mesoporous silica nanoparticles with a core-cone structure (MSN-CC) has been synthesized. The large cone-shaped pores are formed by silica lamellae closely packed encircling a spherical core, showing a structure similar to the flower dahlia. MSN-CC has a large pore size of 45 nm and a high pore volume of 2.59 cm(3) g(-1). MSN-CC demonstrates a high loading capacity of large proteins and successfully delivers active β-galactosidase into cells, showing their potential as efficient nanocarriers for the cellular delivery of proteins with large molecular weights. PMID:26426420

  15. Large-scale determination of previously unsolved protein structures using evolutionary information.

    PubMed

    Ovchinnikov, Sergey; Kinch, Lisa; Park, Hahnbeom; Liao, Yuxing; Pei, Jimin; Kim, David E; Kamisetty, Hetunandan; Grishin, Nick V; Baker, David

    2015-01-01

    The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder. PMID:26335199

  16. NPHP4 controls ciliary trafficking of membrane proteins and large soluble proteins at the transition zone

    PubMed Central

    Awata, Junya; Takada, Saeko; Standley, Clive; Lechtreck, Karl F.; Bellvé, Karl D.; Pazour, Gregory J.; Fogarty, Kevin E.; Witman, George B.

    2014-01-01

    ABSTRACT The protein nephrocystin-4 (NPHP4) is widespread in ciliated organisms, and defects in NPHP4 cause nephronophthisis and blindness in humans. To learn more about the function of NPHP4, we have studied it in Chlamydomonas reinhardtii. NPHP4 is stably incorporated into the distal part of the flagellar transition zone, close to the membrane and distal to CEP290, another transition zone protein. Therefore, these two proteins, which are incorporated into the transition zone independently of each other, define different domains of the transition zone. An nphp4-null mutant forms flagella with nearly normal length, ultrastructure and intraflagellar transport. When fractions from isolated wild-type and nphp4 flagella were compared, few differences were observed between the axonemes, but the amounts of certain membrane proteins were greatly reduced in the mutant flagella, and cellular housekeeping proteins >50 kDa were no longer excluded from mutant flagella. Therefore, NPHP4 functions at the transition zone as an essential part of a barrier that regulates both membrane and soluble protein composition of flagella. The phenotypic consequences of NPHP4 mutations in humans likely follow from protein mislocalization due to defects in the transition zone barrier. PMID:25150219

  17. 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

  18. 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.

  19. A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

    PubMed

    Savitski, Mikhail M; Wilhelm, Mathias; Hahne, Hannes; Kuster, Bernhard; Bantscheff, Marcus

    2015-09-01

    Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target-decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target-decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The "picked" protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The "picked" target-decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used "classic" protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in

  20. Globular clusters, Hipparcos, and the age of the galaxy

    PubMed Central

    Reid, Neill

    1998-01-01

    We discuss the impact of the results from the recent Hipparcos astrometric satellite on distance estimates of galactic globular clusters. Recalibrating the clusters not only implies a relatively small change in the distance to the Large Magellanic Cloud, and hence a rescaling of several estimates of the Hubble constant, but also leads to significantly younger cluster ages. Although the data are not yet conclusive, the results so far point to a likely resolution of the apparent paradox of a universe younger than its constituents, without requiring significant modifications to simple cosmological models. PMID:9419316

  1. 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

    2012-10-01

    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.

  2. 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

    2012-10-01

    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. PMID:23038466

  3. Large-scale identification of membrane proteins with properties favorable for crystallization.

    PubMed

    Kim, Jared; Kagawa, Allison; Kurasaki, Kellie; Ataie, Niloufar; Cho, Il Kyu; Li, Qing X; Ng, Ho Leung

    2015-11-01

    Membrane protein crystallography is notoriously difficult due to challenges in protein expression and issues of degradation and structural stability. We have developed a novel method for large-scale screening of native sources for integral membrane proteins that have intrinsic biochemical properties favorable for crystallization. Highly expressed membrane proteins that are thermally stable and nonaggregating in detergent solutions were identified by mass spectrometry from Escherichia coli, Saccharomyces cerevisiae, and Sus scrofa cerebrum. Many of the membrane proteins identified had been crystallized previously, supporting the promise of the approach. Most identified proteins have known functions and include high-value targets such as transporters and ATPases. To validate the method, we recombinantly expressed and purified the yeast protein, Yop1, which is responsible for endoplasmic reticulum curvature. We demonstrate that Yop1 can be purified with the detergent dodecylmaltoside without aggregating.

  4. Using Globular Clusters to Test Gravity in the Weak Acceleration Regime

    NASA Astrophysics Data System (ADS)

    Scarpa, Riccardo; Marconi, Gianni; Gilmozzi, Roberto; Carraro, Giovanni

    2007-06-01

    We report on the results from an ongoing programme aimed at testing Newton's law of gravity in the low acceleration regime using globular clusters. We find that all clusters studied so far behave like galaxies, that is, their velocity dispersion profiles flatten out at large radii where the acceleration of gravity goes below 10 8 cm s 2, instead of following the expected Keplerian fall-off. In galaxies this behaviour is ascribed to the existence of a dark matter halo. Globular clusters, however, are not supposed to contain dark matter, hence this result might indicate that our present understanding of gravity in the weak regime of accelerations is incomplete and possibly incorrect.

  5. 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.

  6. 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.

  7. Large-scale de novo prediction of physical protein-protein association.

    PubMed

    Elefsinioti, Antigoni; Saraç, Ömer Sinan; Hegele, Anna; Plake, Conrad; Hubner, Nina C; Poser, Ina; Sarov, Mihail; Hyman, Anthony; Mann, Matthias; Schroeder, Michael; Stelzl, Ulrich; Beyer, Andreas

    2011-11-01

    Information about the physical association of proteins is extensively used for studying cellular processes and disease mechanisms. However, complete experimental mapping of the human interactome will remain prohibitively difficult in the near future. Here we present a map of predicted human protein interactions that distinguishes functional association from physical binding. Our network classifies more than 5 million protein pairs predicting 94,009 new interactions with high confidence. We experimentally tested a subset of these predictions using yeast two-hybrid analysis and affinity purification followed by quantitative mass spectrometry. Thus we identified 462 new protein-protein interactions and confirmed the predictive power of the network. These independent experiments address potential issues of circular reasoning and are a distinctive feature of this work. Analysis of the physical interactome unravels subnetworks mediating between different functional and physical subunits of the cell. Finally, we demonstrate the utility of the network for the analysis of molecular mechanisms of complex diseases by applying it to genome-wide association studies of neurodegenerative diseases. This analysis provides new evidence implying TOMM40 as a factor involved in Alzheimer's disease. The network provides a high-quality resource for the analysis of genomic data sets and genetic association studies in particular. Our interactome is available via the hPRINT web server at: www.print-db.org.

  8. 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

  9. Reconstructing galaxy histories from globular clusters

    NASA Astrophysics Data System (ADS)

    West, Michael J.; Côté, Patrick; Marzke, Ronald O.; Jordán, Andrés

    2004-01-01

    Nearly a century after the true nature of galaxies as distant `island universes' was established, their origin and evolution remain great unsolved problems of modern astrophysics. One of the most promising ways to investigate galaxy formation is to study the ubiquitous globular star clusters that surround most galaxies. Globular clusters are compact groups of up to a few million stars. They generally formed early in the history of the Universe, but have survived the interactions and mergers that alter substantially their parent galaxies. Recent advances in our understanding of the globular cluster systems of the Milky Way and other galaxies point to a complex picture of galaxy genesis driven by cannibalism, collisions, bursts of star formation and other tumultuous events.

  10. Reconstructing galaxy histories from globular clusters.

    PubMed

    West, Michael J; Côté, Patrick; Marzke, Ronald O; Jordán, Andrés

    2004-01-01

    Nearly a century after the true nature of galaxies as distant 'island universes' was established, their origin and evolution remain great unsolved problems of modern astrophysics. One of the most promising ways to investigate galaxy formation is to study the ubiquitous globular star clusters that surround most galaxies. Globular clusters are compact groups of up to a few million stars. They generally formed early in the history of the Universe, but have survived the interactions and mergers that alter substantially their parent galaxies. Recent advances in our understanding of the globular cluster systems of the Milky Way and other galaxies point to a complex picture of galaxy genesis driven by cannibalism, collisions, bursts of star formation and other tumultuous events. PMID:14702077

  11. Nova-driven winds in globular clusters

    NASA Technical Reports Server (NTRS)

    Scott, E. H.; Durisen, R. H.

    1978-01-01

    Recent sensitive searches for H-alpha emission from ionized intracluster gas in globular clusters have set upper limits that conflict with theoretical predictions. It is suggested that nova outbursts heat the gas, producing winds that resolve this discrepancy. The incidence of novae in globular clusters, the conversion of kinetic energy of the nova shell to thermal energy of the intracluster gas, and the characteristics of the resultant winds are discussed. Calculated emission from the nova-driven models does not conflict with any observations to date. Some suggestions are made concerning the most promising approaches for future detection of intracluster gas on the basis of these models. The possible relationship of nova-driven winds to globular cluster X-ray sources is also considered.

  12. Reconstructing galaxy histories from globular clusters.

    PubMed

    West, Michael J; Côté, Patrick; Marzke, Ronald O; Jordán, Andrés

    2004-01-01

    Nearly a century after the true nature of galaxies as distant 'island universes' was established, their origin and evolution remain great unsolved problems of modern astrophysics. One of the most promising ways to investigate galaxy formation is to study the ubiquitous globular star clusters that surround most galaxies. Globular clusters are compact groups of up to a few million stars. They generally formed early in the history of the Universe, but have survived the interactions and mergers that alter substantially their parent galaxies. Recent advances in our understanding of the globular cluster systems of the Milky Way and other galaxies point to a complex picture of galaxy genesis driven by cannibalism, collisions, bursts of star formation and other tumultuous events.

  13. SERF: in vitro election of random RNA fragments to identify protein binding sites within large RNAs.

    PubMed

    Stelzl, U; Nierhaus, K H

    2001-11-01

    In vitro selection experiments have various goals depending on the composition of the initial pool and the selection method applied. We developed an in vitro selection variant (SERF, selection of random RNA fragments) that is useful for the identification of short RNA fragments originating from large RNAs that bind specifically to a protein. A pool of randomly fragmented RNA is constructed from a large RNA, which is the natural binding partner for a protein. Such a pool contains all the potential binding sites and is therefore used as starting material for affinity selection with the purified protein to find its natural target. Here we provide a detailed experimental protocol of the method. SERF has been developed for ribosomal systems and is a general approach providing a basis for functional and structural characterization of RNA-protein interactions in large ribonucleoprotein particles.

  14. Millisecond radio pulsars in globular clusters

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  15. Large-scale identification of encystment-related proteins and genes in Pseudourostyla cristata

    PubMed Central

    Gao, Xiuxia; Chen, Fenfen; Niu, Tao; Qu, Ruidan; Chen, Jiwu

    2015-01-01

    The transformation of a ciliate into cyst is an advance strategy against an adverse situation. However, the molecular mechanism for the encystation of free-living ciliates is poorly understood. A large-scale identification of the encystment-related proteins and genes in ciliate would provide us with deeper insights into the molecular mechanisms for the encystations of ciliate. We identified the encystment-related proteins and genes in Pseudourostyla cristata with shotgun LC-MS/MS and scale qRT-PCR, respectively, in this report. A total of 668 proteins were detected in the resting cysts, 102 of these proteins were high credible proteins, whereas 88 high credible proteins of the 724 total proteins were found in the vegetative cells. Compared with the vegetative cell, 6 specific proteins were found in the resting cyst. However, the majority of high credible proteins in the resting cyst and the vegetative cell were co-expressed. We compared 47 genes of the co-expressed proteins with known functions in both the cyst and the vegetative cell using scale qRT-PCR. Twenty-seven of 47 genes were differentially expressed in the cyst compared with the vegetative cell. In our identifications, many uncharacterized proteins were also found. These results will help reveal the molecular mechanism for the formation of cyst in ciliates. PMID:26079518

  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. 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

  18. The IMF of Globular Clusters

    NASA Astrophysics Data System (ADS)

    De Marchi, G.; Paresce, F.

    1999-12-01

    Accurate luminosity functions (LF) for a dozen globular clusters have now been measured at or just beyond their half-light radius using HST. They span almost the entire cluster main sequence below 0.75 MO. All these clusters exhibit LF that rise continuously from an absolute I magnitude MI 6 to a peak at MI 8.5-9 and then drop with increasing MI. Transformation of the LF into mass functions (MF) by means of the most recent mass luminosity relations that are consistent with all presently available data on the physical properties of low mass, low metallicity stars shows that all the LF observed so far can be obtained from MF having the shape of a log-normal distribution with characteristic mass mc=0.33 +/- 0.03 MO and standard deviation sigma =1.81 +/- 0.19. In particular, the LF of the four clusters in the sample that extend well beyond the peak luminosity down to close to the Hydrogen burning limit (NGC6341, NGC6397, NGC6752, and NGC6809) can only be reproduced by such distributions and not by a single power-law in the 0.1 - 0.6 MO range. After correction for the effects of mass segregation, the variation of the ratio of the number of higher to lower mass stars with cluster mass or any simple orbital parameter or the expected time to disruption recently computed for these clusters shows no statistically significant trend over a range of this last parameter of more than a factor of 100. We conclude that the global MF of these clusters have not been measurably modified by evaporation and tidal interactions with the Galaxy and, thus, should reflect the initial distribution of stellar masses. Since the log-normal function that we find is also very similar to the one obtained independently for much younger clusters and to the form expected theoretically, the implication seems to be unavoidable that it represents the true stellar IMF for this type of stars in this mass range.

  19. Crystallization of the large membrane protein complex photosystem I in a microfluidic channel.

    PubMed

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

    2013-12-23

    Traditional macroscale protein crystallization is accomplished nontrivially 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.

  20. 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

  1. 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

  2. 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

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

    PubMed

    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

  4. Myrosinase-binding proteins are derived from a large wound-inducible and repetitive transcript.

    PubMed

    Taipalensuu, J; Falk, A; Ek, B; Rask, L

    1997-02-01

    Several non-myrosinase proteins have been found in association with some of the myrosinases extracted from rape (Brassica napus) seed. Most of these proteins seemed to belong to a large family of proteins ranging in size over approximately 30-110 kDa, namely the myrosinase-binding protein (MBP) family. Potentially all of these MBPs might be derived from a single large precursor, encoded by a 3.3-kb transcript. This transcript coded for a 99-kDa glycine-rich protein with a highly repetitive structure. The mature 50-kDa and 52-kDa MBP amino-terminal was located 255 amino acids from the putative initiation methionine. Also, a more divergently related transcript, the protein product of which was unknown, has been cloned. However, the largest open reading frame suggested a proline-rich protein. While this transcript seemed to be expressed predominantly in seeds, the MBP transcripts were expressed in several tissues and also exhibited a responsiveness to wounding and methyl jasmonate. Both proteins exhibited significant similarities to lectins from Artocarpus integer and from Maclura pomifera.

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

    PubMed

    Dai, Liang; Zhou, Yaoqi

    2011-05-01

    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 (MLPs). 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 domains from structural classification of protein domains reproduces those existing structural clusters (63%) mostly as hubs for many nonredundant 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-size 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 new-fold targets from critical assessment of structure prediction techniques (CASP) by MLP on template-based structure prediction is also discussed. Our MLP structures are available for download at the publication page of the

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

    PubMed Central

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

    2015-01-01

    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. PMID:25977292

  8. Dynamical Coupling of Intrinsically Disordered Proteins and Their Hydration Water: Comparison with Folded Soluble and Membrane Proteins

    PubMed Central

    Gallat, F.-X.; Laganowsky, A.; Wood, K.; Gabel, F.; van Eijck, L.; Wuttke, J.; Moulin, M.; Härtlein, M.; Eisenberg, D.; Colletier, J.-P.; Zaccai, G.; Weik, M.

    2012-01-01

    Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context. PMID:22828339

  9. 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.

  10. Transdermal immunization with large proteins by means of ultradeformable drug carriers.

    PubMed

    Paul, A; Cevc, G; Bachhawat, B K

    1995-12-01

    By means of novel, ultradeformable and self-optimizing agent carriers called transfersomes, large molecules can be brought into the body through intact permeability barriers. This permits non-invasive immunization through normal skin and gives rise to a similar or even slightly higher antibody titer than subcutaneous injections of the same immunogen formulation. The former type of immunization also results in a higher IgA/IgG ratio in the blood than the repeated immunogen injections, as shown here for a soluble protein, human serum albumin, as well as for an integral membrane protein, gap junction protein, in mice.

  11. 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.

  12. 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

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

    PubMed

    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

  14. 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

  15. 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.

  16. 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)

  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. 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

  19. Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry*

    PubMed Central

    Reiter, Lukas; Claassen, Manfred; Schrimpf, Sabine P.; Jovanovic, Marko; Schmidt, Alexander; Buhmann, Joachim M.; Hengartner, Michael O.; Aebersold, Ruedi

    2009-01-01

    Comprehensive characterization of a proteome is a fundamental goal in proteomics. To achieve saturation coverage of a proteome or specific subproteome via tandem mass spectrometric identification of tryptic protein sample digests, proteomics data sets are growing dramatically in size and heterogeneity. The trend toward very large integrated data sets poses so far unsolved challenges to control the uncertainty of protein identifications going beyond well established confidence measures for peptide-spectrum matches. We present MAYU, a novel strategy that reliably estimates false discovery rates for protein identifications in large scale data sets. We validated and applied MAYU using various large proteomics data sets. The data show that the size of the data set has an important and previously underestimated impact on the reliability of protein identifications. We particularly found that protein false discovery rates are significantly elevated compared with those of peptide-spectrum matches. The function provided by MAYU is critical to control the quality of proteome data repositories and thereby to enhance any study relying on these data sources. The MAYU software is available as standalone software and also integrated into the Trans-Proteomic Pipeline. PMID:19608599

  20. 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

  1. Large-scale determination of previously unsolved protein structures using evolutionary information

    PubMed Central

    Ovchinnikov, Sergey; Kinch, Lisa; Park, Hahnbeom; Liao, Yuxing; Pei, Jimin; Kim, David E; Kamisetty, Hetunandan; Grishin, Nick V; Baker, David

    2015-01-01

    The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue–residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder. DOI: http://dx.doi.org/10.7554/eLife.09248.001 PMID:26335199

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

    PubMed

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

    2013-11-01

    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.

  3. Isolated elliptical galaxies, their globular cluster systems, and LCDM

    NASA Astrophysics Data System (ADS)

    Lane, Richard; Salinas, Ricardo; Richtler, Tom

    2015-08-01

    The globular cluster (GC) systems of isolated elliptical galaxies (IEs) have only recently begun to be studied in detail, and may exhibit morphological connections to the evolutionary histories of their hosts. In fact evidence is mounting that the GC systems of massive galaxies in clusters are largely assembled by infall/accretion processes. IEs are their counterparts in low density environments and a comparison of their GC systems should directly highlight environmental effects. Are GCs the answer to unlocking the evolution of isolated galaxies? In addition, the GC systems of reasonably nearby galaxies are detectable out to large radii, making them useful tracers for producing dynamical models of their hosts. How much dark matter is contained within IEs? Very little it seems, at least in some cases. GCs are, therefore, also one of the most important tools we have for testing Lambda CDM models observationally.

  4. Large, dynamic, multi-protein complexes: a challenge for structural biology.

    PubMed

    Różycki, Bartosz; Boura, Evzen

    2014-11-19

    Structural biology elucidates atomic structures of macromolecules such as proteins, DNA, RNA, and their complexes to understand the basic mechanisms of their functions. Among proteins that pose the most difficult problems to current efforts are those which have several large domains connected by long, flexible polypeptide segments. Although abundant and critically important in biological cells, such proteins have proven intractable by conventional techniques. This gap has recently led to the advancement of hybrid methods that use state-of-the-art computational tools to combine complementary data from various high- and low-resolution experiments. In this review, we briefly discuss the individual experimental techniques to illustrate their strengths and limitations, and then focus on the use of hybrid methods in structural biology. We describe how representative structures of dynamic multi-protein complexes are obtained utilizing the EROS hybrid method that we have co-developed. PMID:25335513

  5. Large, dynamic, multi-protein complexes: a challenge for structural biology

    NASA Astrophysics Data System (ADS)

    Różycki, Bartosz; Boura, Evzen

    2014-11-01

    Structural biology elucidates atomic structures of macromolecules such as proteins, DNA, RNA, and their complexes to understand the basic mechanisms of their functions. Among proteins that pose the most difficult problems to current efforts are those which have several large domains connected by long, flexible polypeptide segments. Although abundant and critically important in biological cells, such proteins have proven intractable by conventional techniques. This gap has recently led to the advancement of hybrid methods that use state-of-the-art computational tools to combine complementary data from various high- and low-resolution experiments. In this review, we briefly discuss the individual experimental techniques to illustrate their strengths and limitations, and then focus on the use of hybrid methods in structural biology. We describe how representative structures of dynamic multi-protein complexes are obtained utilizing the EROS hybrid method that we have co-developed.

  6. 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.

  7. Detecting remote evolutionary relationships among proteins by large-scale semantic embedding.

    PubMed

    Melvin, Iain; Weston, Jason; Noble, William Stafford; Leslie, Christina

    2011-01-01

    Virtually every molecular biologist has searched a protein or DNA sequence database to find sequences that are evolutionarily related to a given query. Pairwise sequence comparison methods--i.e., measures of similarity between query and target sequences--provide the engine for sequence database search and have been the subject of 30 years of computational research. For the difficult problem of detecting remote evolutionary relationships between protein sequences, the most successful pairwise comparison methods involve building local models (e.g., profile hidden Markov models) of protein sequences. However, recent work in massive data domains like web search and natural language processing demonstrate the advantage of exploiting the global structure of the data space. Motivated by this work, we present a large-scale algorithm called ProtEmbed, which learns an embedding of protein sequences into a low-dimensional "semantic space." Evolutionarily related proteins are embedded in close proximity, and additional pieces of evidence, such as 3D structural similarity or class labels, can be incorporated into the learning process. We find that ProtEmbed achieves superior accuracy to widely used pairwise sequence methods like PSI-BLAST and HHSearch for remote homology detection; it also outperforms our previous RankProp algorithm, which incorporates global structure in the form of a protein similarity network. Finally, the ProtEmbed embedding space can be visualized, both at the global level and local to a given query, yielding intuition about the structure of protein sequence space.

  8. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR.

    PubMed

    Damianov, Andrey; Ying, Yi; Lin, Chia-Ho; Lee, Ji-Ann; Tran, Diana; Vashisht, Ajay A; Bahrami-Samani, Emad; Xing, Yi; Martin, Kelsey C; Wohlschlegel, James A; Black, Douglas L

    2016-04-21

    Rbfox proteins control alternative splicing and posttranscriptional regulation in mammalian brain and are implicated in neurological disease. These proteins recognize the RNA sequence (U)GCAUG, but their structures and diverse roles imply a variety of protein-protein interactions. We find that nuclear Rbfox proteins are bound within a large assembly of splicing regulators (LASR), a multimeric complex containing the proteins hnRNP M, hnRNP H, hnRNP C, Matrin3, NF110/NFAR-2, NF45, and DDX5, all approximately equimolar to Rbfox. We show that splicing repression mediated by hnRNP M is stimulated by Rbfox. Virtually all the intron-bound Rbfox is associated with LASR, and hnRNP M motifs are enriched adjacent to Rbfox crosslinking sites in vivo. These findings demonstrate that Rbfox proteins bind RNA with a defined set of cofactors and affect a broader set of exons than previously recognized. The function of this multimeric LASR complex has implications for deciphering the regulatory codes controlling splicing networks.

  9. Multiple populations in globular clusters. Lessons learned from the Milky Way globular clusters

    NASA Astrophysics Data System (ADS)

    Gratton, Raffaele G.; Carretta, Eugenio; Bragaglia, Angela

    2012-02-01

    Recent progress in studies of globular clusters has shown that they are not simple stellar populations, but rather are made up of multiple generations. Evidence stems both from photometry and spectroscopy. A new paradigm is arising for the formation of massive star clusters, which includes several episodes of star formation. While this provides an explanation for several features of globular clusters, including the second-parameter problem, it also opens new perspectives on the relation between globular clusters and the halo of our Galaxy, and by extension on all populations with a high specific frequency of globular clusters, such as, e.g., giant elliptical galaxies. We review progress in this area, focussing on the most recent studies. Several points remain to become properly understood, in particular those concerning the nature of the polluters producing the abundance pattern in the clusters and the typical timescale, the range of cluster masses where this phenomenon is active, and the relation between globular clusters and other satellites of our Galaxy.

  10. 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.

  11. Globular Clusters in the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Bica, E.; Ortolani, S.; Barbuy, B.

    2016-06-01

    A view of the Galactic bulge by means of their globular clusters is fundamental for a deep understanding of its formation and evolution. Connections between the globular cluster and field star properties in terms of kinematics, orbits, chemical abundances, and ages should shed light on different stellar population components. Based on spatial distribution and metallicity, we define a probable best list of bulge clusters, containing 43 entries. Future work on newly discovered objects, mostly from the VVV survey, is suggested. These candidates might alleviate the issue of missing clusters on the far side of the bulge. We discuss the reddening law affecting the cluster distances towards the centre of the Galaxy, and conclude that the most suitable total-to-selective absorption value appears to be R V=3.2, in agreement with recent analyses. An update of elemental abundances for bulge clusters is provided.

  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. UNCLOAKING GLOBULAR CLUSTERS IN THE INNER GALAXY

    SciTech Connect

    Alonso-Garcia, Javier; Catelan, Marcio; Minniti, Dante; Mateo, Mario; Sen, Bodhisattva; Banerjee, Moulinath; Von Braun, Kaspar E-mail: mcatelan@astro.puc.cl E-mail: mmateo@umich.edu E-mail: moulib@umich.edu

    2012-03-15

    Extensive photometric studies of the globular clusters located toward the center of the Milky Way have been historically neglected. The presence of patchy differential reddening in front of these clusters has proven to be a significant obstacle to their detailed study. We present here a well defined and reasonably homogeneous photometric database for 25 of the brightest Galactic globular clusters located in the direction of the inner Galaxy. These data were obtained in the B, V, and I bands using the Magellan 6.5 m Telescope and the Hubble Space Telescope. A new technique is extensively used in this paper to map the differential reddening in the individual cluster fields, and to produce cleaner, dereddened color-magnitude diagrams for all the clusters in the database. Subsequent papers will detail the astrophysical analysis of the cluster populations, and the properties of the obscuring material along the clusters' lines of sight.

  14. 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. PMID:27391278

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

    PubMed

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

    2016-01-01

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

  16. 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

  17. 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.

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

    PubMed

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

    2009-08-14

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

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

    PubMed

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

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

  20. Establishment and characterization of human engineered cells stably expressing large extracellular matrix proteins.

    PubMed

    Kwon, Daekee; Kang, Gwang-Sik; Han, Dong Keun; Park, Kwideok; Kim, Jae-Hwan; Lee, Soo-Hong

    2014-01-01

    Commercially available extracellular matrix (ECM) hydrogel-coated culture plates have been used to study the relationship between the ECM microenvironment and stem cell behavior. However, it is unclear whether ECM-coated dishes mimic the natural ECM microenvironment because the architecture of the ECM is constructed of randomly distributed fibers. The purpose of this study was the production and confirmation of human engineered cell lines stably expressing large ECM proteins such as collagen I/II and fibronectin. First, large (over 10 kb) ECM vectors encoding human collagen I/II and fibronectin were constructed and the circular vectors were linearized. Second, the linear ECM vectors were introduced into immortalized human embryonic kidney cells using various transfection methods. The polyethylenimine and liposome methods showed higher efficiencies than electroporation for transfection of these large vectors. Third, human ECM engineered cells were established by stable integration of the vector into the genomic DNA and resulted in stable overexpression of mRNA and proteins. In summary, human engineered cell lines stably expressing large ECM proteins such as human collagen I/II and fibronectin were successfully prepared, and secretion of the ECM components into the surrounding environment was confirmed by immunocytochemistry. Thus, human ECM engineered cells naturally secreting ECM components could be valuable for studying the relationship between the native ECM microenvironment and stem cell behavior.

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

    PubMed Central

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

    2014-01-01

    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 multiple genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL) 1. 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 2–6. Consequently, many eQTL are likely missed, especially those with smaller effects 7. Further, most studies use mRNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics 8–13 reported surprising differences between eQTL and protein QTL (pQTL) for the same genes 9,10, 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 Saccharomyes 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 vs. 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 cluster at hotspot locations that influence multiple proteins—in some cases, more than half of those examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell physiology between yeast strains. PMID:24402228

  2. 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.

  3. 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.

  4. 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.

  5. Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals

    PubMed Central

    Popadin, Konstantin; Polishchuk, Leonard V.; Mamirova, Leila; Knorre, Dmitry; Gunbin, Konstantin

    2007-01-01

    After the effective size of a population, Ne, declines, some slightly deleterious amino acid replacements which were initially suppressed by purifying selection become effectively neutral and can reach fixation. Here we investigate this phenomenon for a set of all 13 mitochondrial protein-coding genes from 110 mammalian species. By using body mass as a proxy for Ne, we show that large mammals (i.e., those with low Ne) as compared with small ones (in our sample these are, on average, 369.5 kg and 275 g, respectively) have a 43% higher rate of accumulation of nonsynonymous nucleotide substitutions relative to synonymous substitutions, and an 8–40% higher rate of accumulation of radical amino acid substitutions relative to conservative substitutions, depending on the type of amino acid classification. These higher rates result in a 6% greater amino acid dissimilarity between modern species and their most recent reconstructed ancestors in large versus small mammals. Because nonsynonymous substitutions are likely to be more harmful than synonymous substitutions, and radical amino acid substitutions are likely to be more harmful than conservative ones, our results suggest that large mammals experience less efficient purifying selection than small mammals. Furthermore, because in the course of mammalian evolution body size tends to increase and, consequently, Ne tends to decline, evolution of mammals toward large body size may involve accumulation of slightly deleterious mutations in mitochondrial protein-coding genes, which may contribute to decline or extinction of large mammals. PMID:17679693

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

    PubMed

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

    2016-09-01

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

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

    DOEpatents

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

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

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

    PubMed

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

    2016-09-01

    Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches. PMID:27154509

  9. Astrometry and photometry in the globular cluster M2

    NASA Astrophysics Data System (ADS)

    Cudworth, Kyle M.; Rauscher, Bernard J.

    1987-04-01

    Proper motions and photometry have been obtained for 301 stars down to V = about 16 in the region of the globular cluster M2. Membership probabilities derived from the proper motions show that over 200 of these stars are highly probable cluster members, including a number of UV-bright stars. A few stars suspected of being field stars in a recent dynamical study of the cluster of Pryor et al. (1986) are confirmed to be nonmembers. The internal proper-motion dispersion has been detected and is clearly isotropic out to about 3 arcmin from the cluster center. The proper-motion and radial-velocity dispersions have been equated to yield a distance of 11.0 + or - 1.7 kpc independent of any standard-candle assumptions. An accurate position of the cluster center has been measured that differs markedly from that found by Shawl and White (1986). A large space velocity has been derived for the cluster.

  10. 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.

  11. Rapid assignment of solution 31P NMR spectra of large proteins by solid-state spectroscopy.

    PubMed

    Iuga, Adriana; Spoerner, Michael; Ader, Christian; Brunner, Eike; Kalbitzer, Hans Robert

    2006-07-21

    The application of the (31)P NMR spectroscopy to large proteins or protein complexes in solution is hampered by a relatively low intrinsic sensitivity coupled with large line widths. Therefore, the assignment of the phosphorus signals by two-dimensional NMR methods in solution is often extremely time consuming. In contrast, the quality of solid-state NMR spectra is not dependent on the molecular mass and the solubility of the protein. For the complex of Ras with the GTP-analogue GppCH(2)p we show solid-state (31)P NMR methods to be more sensitive by almost one order of magnitude than liquid-state NMR. Thus, solid-state NMR seems to be the method of choice for obtaining the resonance assignment of the phosphorus signals of protein complexes in solution. Experiments on Ras.GDP complexes show that the microcrystalline sample can be substituted by a precipitate of the sample and that unexpectedly the two structural states observed earlier in solution are present in crystals as well.

  12. 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

  13. 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

  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. 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.

  16. Investigation of multiple stellar populations in globular clusters with the Sloan Digital Sky Survey

    NASA Astrophysics Data System (ADS)

    Smolinski, Jason P.

    This dissertation describes the study of abundance variations among stars in Galactic globular clusters using the large set of spectroscopic data collected by the Sloan Digital Sky Survey (SDSS). Globular clusters have typically been considered to be simple stellar populations---groups of stars that are coeval and chemically homogeneous. Observations within the last forty years have shed light on the possibility that they are not so simple after all by revealing the presence of star-to-star variations in light-element abundances. Additionally, several globular clusters are known to harbor multiple populations of stars by the presence of multiple sequences on a color-magnitude diagram. In this study, the procedure for membership selection is first described. Stars are selected from the vast data set available from SDSS Data Release 7 and several cuts are made to reduce the sample down to only those stars that are members of the globular clusters in this sample. This procedure is also performed on three open clusters as well and is further used to validate the current SEGUE Stellar Parameter Pipeline. CN and CH molecular absorption indices are then measured for all globular cluster member stars and their distributions are analyzed. Bimodal distributions in CN are seen on the red giant branch in all clusters with [Fe/H] > -2.1, and hints of bimodality are seen for two metal-poor clusters as well. CN-CH anticorrelations are also seen and the implications are discussed. The observed distributions of CN absorption bandstrengths are examined and compared to theoretical predictions from two-population models. These results are combined with radial distributions and positions on the color-magnitude diagram as evidence for the presence of multiple populations of stars within the clusters in this sample.

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

    PubMed Central

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

    2015-01-01

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

  18. A large scale membrane-binding protein conformational change that initiates at small length scales

    NASA Astrophysics Data System (ADS)

    Grandpre, Trevor; Andorf, Matthew; Chakravarthy, Srinivas; Lamb, Robert; Poor, Taylor; Landahl, Eric

    2013-03-01

    The fusion (F) protein of parainfluenza virus 5 (PIV5) is a membrane-bound, homotrimeric glycoprotein located on the surface of PIV5 viral envelopes. Upon being triggered by the receptor-binding protein (HN), F undergoes a greater than 100Å ATP-independent refolding event. This refolding event results in the insertion of a hydrophobic fusion peptide into the membrane of the target cell, followed by the desolvation and subsequent fusion event as the two membranes are brought together. Isothermal calorimetry and hydrophobic dye incorporation experiments indicate that the soluble construct of the F protein undergoes a conformational rearrangement event at around 55 deg C. We present the results of an initial Time-Resolved Small-Angle X-Ray Scattering (TR-SAXS) study of this large scale, entropically driven conformational change using a temperature jump. Although we the measured radius of gyration of this protein changes on a 110 second timescale, we find that the x-ray scattering intensity at higher angles (corresponding to smaller length scales in the protein) changes nearly an order of magnitude faster. We believe this may be a signature of entropically-driven conformational change. To whom correspondence should be addressed

  19. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies

    PubMed Central

    Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H.; Michel, Jennifer Carlisle; Claxton, Derek P.; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K. Christopher; Gouaux, Eric

    2014-01-01

    Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in over-expression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol we show how to use small-scale transient transfection and fluorescence-detection, size-exclusion chromatography (FSEC) experiments using a GFP-His8 tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI− (N-acetylglucosaminyltransferase I-negative) cells in suspension culture, and over-express the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl), for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks. PMID:25299155

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  3. Isolation, cloning and large scale expression of glutathione-S-transferase (GST) protein of Polymyxa betae.

    PubMed

    Safarpour, H; Safarnejad, M R

    2012-01-01

    The plasmodiophoromycete Polymyxa betae, an obligate parasite of sugar-beet roots, is a natural vector of Beet necrotic yellow vein virus (BNYVV). To develop protein based diagnosis for any pathogenic agents including P. betae, a specific immunogenic protein has to be prepared. The glutathione-S-transferase (GST) is expressed in all the morphologically different stages of the pathogen's life cycle, and then it is a good candidate as an immunogenic agent for developing of specific antibodies and diagnostic purposes. The present study describes isolation, cloning and large scale expression and purification of P. betae GST protein. For this aim, total RNA was initially isolated from infected plants and corresponding cDNA was constructed by using reverse transcriptase and oligo-dT primer as well as mRNA as a template. The gene encoding GST was isolated and PCR-amplified from the synthesized cDNA by using specific primers. The amplified fragments were preliminary cloned into pTZ57R/T cloning vector. Intact clone containing right sequence was selected after digestion, PCR amplification and subsequent sequencing analysis. Next, GST encoding region having right sequence was recovered and sub-cloned into pET28a bacterial expression vector. Large scale expression of recombinant protein was performed in BL21-de3 strain of E. coli and purification was carried out under native situation through Immobolized metal ion affinity chromatography (IMAC) in column containing Ni-NTA agarose beads. Successful expression and purification steps were confirmed by SDS-PAGE followed by western blotting analysis. These results confirmed the high purity and integrity of GST protein which was around 21 kDa. Generally, the total yield of the purified protein in the culture medium was estimated at around 3.5 mg/mL. After purification, a major part of the purified proteins was precipitated identified as excess GST. To improve the solubility, the final concentration of purified protein was reduced

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

    PubMed Central

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

    2016-01-01

    Bacillus thuringiensis (Bt) Cyt2Aa2 showed toxicity against Dipteran insect larvae and in vitro lysis activity on several cells. It has potential applications in the biological control of insect larvae. Although pore-forming and/or detergent-like mechanisms were proposed, the mechanism underlying cytolytic activity remains unclear. Analysis of the haemolytic activity of Cyt2Aa2 with osmotic stabilizers revealed partial toxin inhibition, suggesting a distinctive mechanism from the putative pore formation model. Membrane permeability was studied using fluorescent dye entrapped in large unilamellar vesicles (LUVs) at various protein/lipid molar ratios. Binding of Cyt2Aa2 monomer to the lipid membrane did not disturb membrane integrity until the critical protein/lipid molar ratio was reached, when Cyt2Aa2 complexes and cytolytic activity were detected. The complexes are large aggregates that appeared as a ladder when separated by agarose gel electrophoresis. Interaction of Cyt2Aa2 with Aedes albopictus cells was investigated by confocal microscopy and total internal reflection fluorescent microscopy (TIRF). The results showed that Cyt2Aa2 binds on the cell membrane at an early stage without cell membrane disruption. Protein aggregation on the cell membrane was detected later which coincided with cell swelling. Cyt2Aa2 aggregations on supported lipid bilayers (SLBs) were visualized by AFM. The AFM topographic images revealed Cyt2Aa2 aggregates on the lipid bilayer at low protein concentration and subsequently disrupts the lipid bilayer by forming a lesion as the protein concentration increased. These results supported the mechanism whereby Cyt2Aa2 binds and aggregates on the lipid membrane leading to the formation of non-specific hole and disruption of the cell membrane. PMID:27612497

  5. Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins.

    PubMed

    Das, B; Meirovitch, H; Navon, I M

    2003-07-30

    Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited-memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computat Opt Appl 2002, 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all-atom AMBER force field with a dielectric constant epsilon = 1 and a distance-dependent dielectric function epsilon = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from epsilon = 2r to epsilon = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial-and-error calculations for each problem.

  6. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes

    NASA Astrophysics Data System (ADS)

    Lu, Jonathan; Trnka, Michael J.; Roh, Soung-Hun; Robinson, Philip J. J.; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L.; Guan, Shenheng

    2015-12-01

    Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise.

  7. Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

    SciTech Connect

    Galat, Andrzej Thai, Robert

    2014-08-08

    Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

  8. Large scale crystallization of protein pharmaceuticals in microgravity via temperature change

    NASA Technical Reports Server (NTRS)

    Long, Marianna M.

    1992-01-01

    The major objective of this research effort is the temperature driven growth of protein crystals in large batches in the microgravity environment of space. Pharmaceutical houses are developing protein products for patient care, for example, human insulin, human growth hormone, interferons, and tissue plasminogen activator or TPA, the clot buster for heart attack victims. Except for insulin, these are very high value products; they are extremely potent in small quantities and have a great value per gram of material. It is feasible that microgravity crystallization can be a cost recoverable, economically sound final processing step in their manufacture. Large scale protein crystal growth in microgravity has significant advantages from the basic science and the applied science standpoints. Crystal growth can proceed unhindered due to lack of surface effects. Dynamic control is possible and relatively easy. The method has the potential to yield large quantities of pure crystalline product. Crystallization is a time honored procedure for purifying organic materials and microgravity crystallization could be the final step to remove trace impurities from high value protein pharmaceuticals. In addition, microgravity grown crystals could be the final formulation for those medicines that need to be administered in a timed release fashion. Long lasting insulin, insulin lente, is such a product. Also crystalline protein pharmaceuticals are more stable for long-term storage. Temperature, as the initiation step, has certain advantages. Again, dynamic control of the crystallization process is possible and easy. A temperature step is non-invasive and is the most subtle way to control protein solubility and therefore crystallization. Seeding is not necessary. Changes in protein and precipitant concentrations and pH are not necessary. Finally, this method represents a new way to crystallize proteins in space that takes advantage of the unique microgravity environment. The results

  9. 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

  10. 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.

  11. Comments on the Formation of Globular Clusters from Coalesced Clouds.

    PubMed

    Smith

    1999-11-20

    If a substantial fraction of the proto-Galactic halo was constituted of cloudy structures of sizes 1 kpc or larger, then collisions between these clouds would have been common during the infall of the Galaxy. Such collisions would have shaped the properties of the clouds from which globular clusters formed. If Milky Way globular clusters formed from progenitor clouds which in turn had been constructed from the coalescence of smaller cloud structures, then cluster properties that could naturally be accounted for include: (1) the low percentage of stars in globular clusters relative to the halo field, (2) the chemical homogeneity of globular clusters with respect to heavy elements, and (3) the fact that the lowest metallicity globular clusters are not as metal-poor as some halo field stars.

  12. Large-Scale Cultivation of Acidophilic Hyperthermophiles for Recovery of Secreted Proteins

    PubMed Central

    Worthington, Penny; Blum, Paul; Perez-Pomares, Francisco; Elthon, Tom

    2003-01-01

    An electric water heater was modified for large-scale cultivation of aerobic acidophilic hyperthermophiles to enable recovery of secreted proteins. Critical changes included thermostat replacement, redesign of the temperature control circuit, and removal of the cathodic anticorrosion system. These alterations provided accurate temperature and pH control. The bioreactor was used to cultivate selected strains of the archaeon Sulfolobus solfataricus and other species within this genus. Reformulation of a basal salts medium facilitated preparation of large culture volumes and eliminated sterilization-induced precipitation of medium components. Substrate induction of synthesis of the S. solfataricus-secreted alpha-amylase during growth in a defined medium supported the utility of the bioreactor for studies of physiologically regulated processes. An improved purification strategy was developed by using strong cation-exchange chromatography for recovery of the alpha-amylase and the processing of large sample volumes of acidic culture supernatant. These findings should simplify efforts to study acidophilic hyperthermophilic microbes and their secreted proteins. PMID:12514002

  13. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex

    PubMed Central

    Lyumkis, Dmitry; Oliveira dos Passos, Dario; Tahara, Erich B.; Webb, Kristofor; Bennett, Eric J.; Vinterbo, Staal; Potter, Clinton S.; Carragher, Bridget; Joazeiro, Claudio A. P.

    2014-01-01

    All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), composed of the listerin/Ltn1 E3 ubiquitin ligase and cofactors, mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. How RQC recognizes stalled ribosomes and performs its functions has not been understood. Using single-particle cryoelectron microscopy, we have determined the structure of the RQC complex bound to stalled 60S ribosomal subunits. The structure establishes how Ltn1 associates with the large ribosomal subunit and properly positions its E3-catalytic RING domain to mediate nascent chain ubiquitylation. The structure also reveals that a distinguishing feature of stalled 60S particles is an exposed, nascent chain-conjugated tRNA, and that the Tae2 subunit of RQC, which facilitates Ltn1 binding, is responsible for selective recognition of stalled 60S subunits. RQC components are engaged in interactions across a large span of the 60S subunit surface, connecting the tRNA in the peptidyl transferase center to the distally located nascent chain tunnel exit. This work provides insights into a mechanism linking translation and protein degradation that targets defective proteins immediately after synthesis, while ignoring nascent chains in normally translating ribosomes. PMID:25349383

  14. 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.

  15. On the accuracy of protein determination in large biological samples by prompt gamma neutron activation analysis

    NASA Astrophysics Data System (ADS)

    Kasviki, K.; Stamatelatos, I. E.; Yannakopoulou, E.; Papadopoulou, P.; Kalef-Ezra, J.

    2007-10-01

    A prompt gamma neutron activation analysis (PGNAA) facility has been developed for the determination of nitrogen and thus total protein in large volume biological samples or the whole body of small animals. In the present work, the accuracy of nitrogen determination by PGNAA in phantoms of known composition as well as in four raw ground meat samples of about 1 kg mass was examined. Dumas combustion and Kjeldahl techniques were also used for the assessment of nitrogen concentration in the meat samples. No statistically significant differences were found between the concentrations assessed by the three techniques. The results of this work demonstrate the applicability of PGNAA for the assessment of total protein in biological samples of 0.25-1.5 kg mass, such as a meat sample or the body of small animal even in vivo with an equivalent radiation dose of about 40 mSv.

  16. A novel tau mutation, p.K317N, causes globular glial tauopathy

    PubMed Central

    Tacik, Pawel; DeTure, Michael; Lin, Wen-Lang; Contreras, Monica Sanchez; Wojtas, Aleksandra; Hinkle, Kelly M.; Fujioka, Shinsuke; Baker, Matthew C.; Walton, Ronald L.; Carlomagno, Yari; Brown, Patricia H.; Strongosky, Audrey J.; Kouri, Naomi; Murray, Melissa E.; Petrucelli, Leonard; Josephs, Keith A.; Rademakers, Rosa; Ross, Owen A.; Wszolek, Zbigniew K.; Dickson, Dennis W.

    2016-01-01

    Globular glial tauopathy (GGT) are 4-repeat tauopathies neuropathologically characterized by tau-positive, globular glial inclusions, including both globular oligodendroglial inclusions (GOI) and globular astrocytic inclusions (GAI). No mutations have been found in 25 of the 30 GGT cases reported in the literature who have been screened for mutations in microtubule associated protein tau (MAPT). In this report, six patients with GGT (four with subtype III and two with subtype I) were screened for MAPT mutations. They included 4 men and 2 women with a mean age at death of 73 years (55–83 years) and mean age at symptomatic onset of 66 years (50–77 years). Disease duration ranged from 5 to 14 years. All were homozygous for the MAPT H1 haplotype. Three patients had a positive family history of dementia, and a novel MAPT mutation (c.951G>C, p.K317N) was identified in one of them, a patient with subtype III. Recombinant tau protein bearing the lysine-to-asparagine substitution at amino acid residue 317 was used to assess functional significance of the variant on microtubule assembly and tau filament formation. Recombinant p.K317N tau had reduced ability to promote tubulin polymerization. Recombinant 3R and 4R tau bearing the p.K317N mutation showed decreased 3R tau and increased 4R tau filament assembly. These results strongly suggest that the p.K317N variant is pathogenic. Sequencing of MAPT should be considered in patients with GGT and a family history of dementia or movement disorder. Since several individuals in our series had a positive family history but no MAPT mutation, genetic factors other than MAPT may play a role in disease pathogenesis. PMID:25900293

  17. In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces.

    PubMed

    Wu, Zhonghua; Hu, Gang; Yang, Jianyi; Peng, Zhenling; Uversky, Vladimir N; Kurgan, Lukasz

    2015-09-14

    We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins. These result are applicable for proteins involved in interaction with DNA, RNA, and proteins and suggest that disordered proteins and binding regions are less compact and more likely to assume extended shape. We demonstrate that disordered protein binding residues in the interfaces of disordered proteins drive the increase in the per residue area of these interfaces. Our results can be used to predict in silico whether a given protomer from the DNA, RNA or protein complex is likely to be disordered in its unbound form.

  18. A large iris-like expansion of a mechanosensitive channel protein induced by membrane tension

    NASA Technical Reports Server (NTRS)

    Betanzos, Monica; Chiang, Chien-Sung; Guy, H. Robert; Sukharev, Sergei

    2002-01-01

    MscL, a bacterial mechanosensitive channel of large conductance, is the first structurally characterized mechanosensor protein. Molecular models of its gating mechanisms are tested here. Disulfide crosslinking shows that M1 transmembrane alpha-helices in MscL of resting Escherichia coli are arranged similarly to those in the crystal structure of MscL from Mycobacterium tuberculosis. An expanded conformation was trapped in osmotically shocked cells by the specific bridging between Cys 20 and Cys 36 of adjacent M1 helices. These bridges stabilized the open channel. Disulfide bonds engineered between the M1 and M2 helices of adjacent subunits (Cys 32-Cys 81) do not prevent channel gating. These findings support gating models in which interactions between M1 and M2 of adjacent subunits remain unaltered while their tilts simultaneously increase. The MscL barrel, therefore, undergoes a large concerted iris-like expansion and flattening when perturbed by membrane tension.

  19. Edades relativas de cúmulos globulares

    NASA Astrophysics Data System (ADS)

    Miller Bertolami, M.; Forte, J. C.

    El trabajo de Rossemberg et al (1999), estudia las edades relativas de cúmulos globulares galácticos mediante el análisis de ciertos parámetros morfológicos de los diagramas color-magnitud de dichos cúmulos. Este trabajo se centra en tres puntos: analizar la consistencia de los resultados obtenidos por Rossemberg et al (1999) al emplear observaciones en el sistema fotométrico de Washington, más precisamente, las magnitudes C y T1 en lugar de las magnitudes V e I utilizadas por dichos autores. De la existencia de colores integrados, metalicidad y edad (relativa) para 21 de los cúmulos utilizados en dicho trabajo, se analiza la consistencia de estos resultados con las dependencias de color integrado como función de la edad y la metalicidad que se desprenden de los modelos teóricos de luz integrada por Worthey (1994), Schulz (2002) y Lee et al (2002). Por último se lleva a cabo una breve comparación de la morfología de los diagramas color-magnitud de los cúmulos globulares y de las isocronas utilizadas, a fin de intentar identificar algunas de las posibles causas de las diferencias observadas en los incisos anteriores.

  20. Mapping the differential reddening in globular clusters.

    NASA Astrophysics Data System (ADS)

    Bonatto, C.; Campos, F.; Kepler, S. O.

    Differential-reddening maps for 66 Galactic globular clusters (GCs) are built with archival HST WFC/ACS F606W and F814W photometry. We divide the WFC/ACS field of view across each cluster in a regular cell grid and extract the stellar-density Hess diagram from each cell. Shifts in colour and magnitude along the reddening vector are applied until a match with the mean diagram is obtained. The maps correspond to the internal dispersion of the reddening around the mean. We detect spatially-variable extinction in the 66 globular clusters studied, with mean values ranging from mbox {łangle{\\dEBV}\\rangle}approx0.018 (NGC 6981) up to mbox {łangle{\\dEBV}\\rangle}approx0.16 (Palomar 2). Differential-reddening correction decreases the observed foreground reddening and the apparent distance modulus but, since they are related to the same value of E(B-V), the distance to the Sun is conserved. While the foreground E(B-V) increases rather steeply towards the Galactic plane, <{dEBV >} does the same with a much flatter slope, thus suggesting that part of the measured DR originates inside the clusters. However, the lack of systematic variations of <{dEBV >} with the sampled cluster area indicates that most of the differential reddening is interstellar.

  1. Neutrino and axion bounds from the globular cluster M5 (NGC 5904).

    PubMed

    Viaux, N; Catelan, M; Stetson, P B; Raffelt, G G; Redondo, J; Valcarce, A A R; Weiss, A

    2013-12-01

    The red-giant branch (RGB) in globular clusters is extended to larger brightness if the degenerate helium core loses too much energy in "dark channels." Based on a large set of archival observations, we provide high-precision photometry for the Galactic globular cluster M5 (NGC 5904), allowing for a detailed comparison between the observed tip of the RGB with predictions based on contemporary stellar evolution theory. In particular, we derive 95% confidence limits of g(ae)<4.3×10(-13) on the axion-electron coupling and μ(ν)<4.5×10(-12)μ(B) (Bohr magneton μ(B)=e/2m(e)) on a neutrino dipole moment, based on a detailed analysis of statistical and systematic uncertainties. The cluster distance is the single largest source of uncertainty and can be improved in the future. PMID:24476250

  2. Neutrino and axion bounds from the globular cluster M5 (NGC 5904).

    PubMed

    Viaux, N; Catelan, M; Stetson, P B; Raffelt, G G; Redondo, J; Valcarce, A A R; Weiss, A

    2013-12-01

    The red-giant branch (RGB) in globular clusters is extended to larger brightness if the degenerate helium core loses too much energy in "dark channels." Based on a large set of archival observations, we provide high-precision photometry for the Galactic globular cluster M5 (NGC 5904), allowing for a detailed comparison between the observed tip of the RGB with predictions based on contemporary stellar evolution theory. In particular, we derive 95% confidence limits of g(ae)<4.3×10(-13) on the axion-electron coupling and μ(ν)<4.5×10(-12)μ(B) (Bohr magneton μ(B)=e/2m(e)) on a neutrino dipole moment, based on a detailed analysis of statistical and systematic uncertainties. The cluster distance is the single largest source of uncertainty and can be improved in the future.

  3. A constraint logic programming approach to associate 1D and 3D structural components for large protein complexes.

    PubMed

    Dal Palù, Alessandro; Pontelli, Enrico; He, Jing; Lu, Yonggang

    2007-01-01

    The paper describes a novel framework, constructed using Constraint Logic Programming (CLP) and parallelism, to determine the association between parts of the primary sequence of a protein and alpha-helices extracted from 3D low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

  4. A large family of divergent Drosophila odorant-binding proteins expressed in gustatory and olfactory sensilla.

    PubMed

    Galindo, K; Smith, D P

    2001-11-01

    We identified a large family of putative odorant-binding protein (OBP) genes in the genome of Drosophila melanogaster. Some of these genes are present in large clusters in the genome. Most members are expressed in various taste organs, including gustatory sensilla in the labellum, the pharyngeal labral sense organ, dorsal and ventral cibarial organs, as well as taste bristles located on the wings and tarsi. Some of the gustatory OBPs are expressed exclusively in taste organs, but most are expressed in both olfactory and gustatory sensilla. Multiple binding proteins can be coexpressed in the same gustatory sensillum. Cells in the tarsi that express OBPs are required for normal chemosensation mediated through the leg, as ablation of these cells dramatically reduces the sensitivity of the proboscis extension reflex to sucrose. Finally, we show that OBP genes expressed in the pharyngeal taste sensilla are still expressed in the poxneuro genetic background while OBPs expressed in the labellum are not. These findings support a broad role for members of the OBP family in gustation and olfaction and suggest that poxneuro is required for cell fate determination of labellar but not pharyngeal taste organs. PMID:11729153

  5. mBeRFP, an improved large stokes shift red fluorescent protein.

    PubMed

    Yang, Jie; Wang, Liang; Yang, Fei; Luo, Haiming; Xu, Lingling; Lu, Jinling; Zeng, Shaoqun; Zhang, Zhihong

    2013-01-01

    Herein, we describe the generation of a monomeric large Stokes shift (LSS) red fluorescent protein, mBeRFP, with excitation and emission peaks at 446 and 615 nm, respectively. Compared with two previously reported LSS-RFPs (mKeima and LSS-mKate2), mBeRFP is approximately three times brighter. In addition, mBeRFP is characterized by improved photostability, rapid maturation, an extended lifetime, and a monomeric nature. Additionally, mBeRFP can be paired with the Alexa 647 dye as a FRET donor to detect caspase 3 activity. This FRET pair has an extremely dynamic range and a large Förster radius (approximately 6.5 nm). To demonstrate the applicability of mBeRFP for imaging in living cells, we performed dual-color imaging of mBeRFP and CFP simultaneously excited by a single excitation source, and we demonstrated that these fluorescent proteins allow the clear visualization of the dynamics of Bax during cancer cell apoptosis. Thus, mBeRFP appears to be particularly useful for cellular imaging applications.

  6. Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins.

    PubMed

    Li, Wenfei; Wolynes, Peter G; Takada, Shoji

    2011-03-01

    Proteins have often evolved sequences so as to acquire the ability for regulation via allosteric conformational change. Here we investigate how allosteric dynamics is designed through sequences with nonlinear interaction features. First, for 71 allosteric proteins of which two, open and closed, structures are available, a statistical survey of interactions using an all-atom model with effective solvation shows that those residue contact interactions specific to one of the two states are significantly weaker than are the contact interactions shared by the two states. This interaction feature indicates there is underlying sequence design to facilitate conformational change. Second, based on the energy landscape theory, we implement these interaction features into a new atomic-interaction-based coarse-grained model via a multiscale simulation protocol (AICG). The AICG model outperforms standard coarse-grained models for predictions of the native-state mean fluctuations and of the conformational change direction. Third, using the new model for adenylate kinase, we show that intrinsic fluctuations in one state contain rare and large-amplitude motions nearly reaching the other state. Such large-amplitude motions are realized partly by sequence specificity and partly by the nonlinear nature of contact interactions, leading to cracking. Both features enhance conformational transition rates.

  7. Protein crystal growth in microgravity: Temperature induced large scale crystallization of insulin

    NASA Technical Reports Server (NTRS)

    Long, Marianna M.; Delucas, Larry J.; Smith, C.; Carson, M.; Moore, K.; Harrington, Michael D.; Pillion, D. J.; Bishop, S. P.; Rosenblum, W. M.; Naumann, R. J.

    1994-01-01

    One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macro-molecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjuction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.

  8. The "Globularization Hypothesis" of the Language-ready Brain as a Developmental Frame for Prosodic Bootstrapping Theories of Language Acquisition.

    PubMed

    Irurtzun, Aritz

    2015-01-01

    In recent research (Boeckx and Benítez-Burraco, 2014a,b) have advanced the hypothesis that our species-specific language-ready brain should be understood as the outcome of developmental changes that occurred in our species after the split from Neanderthals-Denisovans, which resulted in a more globular braincase configuration in comparison to our closest relatives, who had elongated endocasts. According to these authors, the development of a globular brain is an essential ingredient for the language faculty and in particular, it is the centrality occupied by the thalamus in a globular brain that allows its modulatory or regulatory role, essential for syntactico-semantic computations. Their hypothesis is that the syntactico-semantic capacities arise in humans as a consequence of a process of globularization, which significantly takes place postnatally (cf. Neubauer et al., 2010). In this paper, I show that Boeckx and Benítez-Burraco's hypothesis makes an interesting developmental prediction regarding the path of language acquisition: it teases apart the onset of phonological acquisition and the onset of syntactic acquisition (the latter starting significantly later, after globularization). I argue that this hypothesis provides a developmental rationale for the prosodic bootstrapping hypothesis of language acquisition (cf. i.a. Gleitman and Wanner, 1982; Mehler et al., 1988, et seq.; Gervain and Werker, 2013), which claim that prosodic cues are employed for syntactic parsing. The literature converges in the observation that a large amount of such prosodic cues (in particular, rhythmic cues) are already acquired before the completion of the globularization phase, which paves the way for the premises of the prosodic bootstrapping hypothesis, allowing babies to have a rich knowledge of the prosody of their target language before they can start parsing the primary linguistic data syntactically. PMID:26696916

  9. The "Globularization Hypothesis" of the Language-ready Brain as a Developmental Frame for Prosodic Bootstrapping Theories of Language Acquisition.

    PubMed

    Irurtzun, Aritz

    2015-01-01

    In recent research (Boeckx and Benítez-Burraco, 2014a,b) have advanced the hypothesis that our species-specific language-ready brain should be understood as the outcome of developmental changes that occurred in our species after the split from Neanderthals-Denisovans, which resulted in a more globular braincase configuration in comparison to our closest relatives, who had elongated endocasts. According to these authors, the development of a globular brain is an essential ingredient for the language faculty and in particular, it is the centrality occupied by the thalamus in a globular brain that allows its modulatory or regulatory role, essential for syntactico-semantic computations. Their hypothesis is that the syntactico-semantic capacities arise in humans as a consequence of a process of globularization, which significantly takes place postnatally (cf. Neubauer et al., 2010). In this paper, I show that Boeckx and Benítez-Burraco's hypothesis makes an interesting developmental prediction regarding the path of language acquisition: it teases apart the onset of phonological acquisition and the onset of syntactic acquisition (the latter starting significantly later, after globularization). I argue that this hypothesis provides a developmental rationale for the prosodic bootstrapping hypothesis of language acquisition (cf. i.a. Gleitman and Wanner, 1982; Mehler et al., 1988, et seq.; Gervain and Werker, 2013), which claim that prosodic cues are employed for syntactic parsing. The literature converges in the observation that a large amount of such prosodic cues (in particular, rhythmic cues) are already acquired before the completion of the globularization phase, which paves the way for the premises of the prosodic bootstrapping hypothesis, allowing babies to have a rich knowledge of the prosody of their target language before they can start parsing the primary linguistic data syntactically.

  10. The mass distribution of the Fornax dSph: constraints from its globular cluster distribution

    NASA Astrophysics Data System (ADS)

    Cole, David R.; Dehnen, Walter; Read, Justin I.; Wilkinson, Mark I.

    2012-10-01

    Uniquely among the dwarf spheroidal (dSph) satellite galaxies of the Milky Way, Fornax hosts globular clusters. It remains a puzzle as to why dynamical friction has not yet dragged any of Fornax's five globular clusters to the centre, and also why there is no evidence that any similar star cluster has been in the past (for Fornax or any other tidally undisrupted dSph). We set up a suite of 2800 N-body simulations that sample the full range of globular cluster orbits and mass models consistent with all existing observational constraints for Fornax. In agreement with previous work, we find that if Fornax has a large dark matter core, then its globular clusters remain close to their currently observed locations for long times. Furthermore, we find previously unreported behaviour for clusters that start inside the core region. These are pushed out of the core and gain orbital energy, a process we call 'dynamical buoyancy'. Thus, a cored mass distribution in Fornax will naturally lead to a shell-like globular cluster distribution near the core radius, independent of the initial conditions. By contrast, cold dark matter-type cusped mass distributions lead to the rapid infall of at least one cluster within Δt = 1-2 Gyr, except when picking unlikely initial conditions for the cluster orbits (˜2 per cent probability), and almost all clusters within Δt = 10 Gyr. Alternatively, if Fornax has only a weakly cusped mass distribution, then dynamical friction is much reduced. While over Δt = 10 Gyr this still leads to the infall of one to four clusters from their present orbits, the infall of any cluster within Δt = 1-2 Gyr is much less likely (with probability 0-70 per cent, depending on Δt and the strength of the cusp). Such a solution to the timing problem requires (in addition to a shallow dark matter cusp) that in the past the globular clusters were somewhat further from Fornax than today; they most likely did not form within Fornax, but were accreted.

  11. Inhibition of bromodomain proteins for the treatment of human diffuse large B-cell lymphoma

    PubMed Central

    Trabucco, Sally E.; Gerstein, Rachel M.; Evens, Andrew M.; Bradner, James E.; Shultz, Leonard D.; Greiner, Dale L.; Zhang, Hong

    2014-01-01

    Purpose Approximately 50% of patients with diffuse large B-cell lymphoma (DLBCL) enter long-term remission after standard chemotherapy. DLBCL patients who do not respond to chemotherapy have few treatment options. There remains a critical need to identify effective and targeted therapeutics for DLBCL. Experimental Design Recent studies have highlighted the incidence of increased c-MYC protein in DLBCL and the correlation between high levels of c-MYC protein and poor survival prognosis of DLBCL patients, suggesting that c-MYC is a compelling target for DLBCL therapy. The small molecule JQ1 suppresses c-MYC expression through inhibition of the bromodomain and extra-terminal (BET) family of bromodomain proteins. We investigated whether JQ1 can inhibit proliferation of DLBCL cells in culture and xenograft models in vivo. Results We show that JQ1 at nanomolar concentrations efficiently inhibited proliferation of human DLBCL cells in a dose-dependent manner regardless of their molecular subtypes, suggesting a broad effect of JQ1 in DLBCL. The initial G1 arrest induced by JQ1 treatment in DLBCL cells was followed by either apoptosis or senescence. The expression of c-MYC was suppressed as a result of JQ1 treatment from the natural, chromosomally-translocated or amplified loci. Furthermore, JQ1 treatment significantly suppressed growth of DLBCL cells engrafted in mice and improved survival of engrafted mice. Conclusion Our results demonstrate that inhibition of the BET family of bromodomain proteins by JQ1 has potential clinical utility in the treatment of DLBCL. PMID:25009295

  12. THE GLOBULAR CLUSTER SYSTEM OF NGC 4636 AND FORMATION OF GLOBULAR CLUSTERS IN GIANT ELLIPTICAL GALAXIES

    SciTech Connect

    Park, Hong Soo; Lee, Myung Gyoon; Hwang, Ho Seong; Kim, Sang Chul; Arimoto, Nobuo; Yamada, Yoshihiko; Tamura, Naoyuki; Onodera, Masato E-mail: mglee@astro.snu.ac.kr E-mail: sckim@kasi.re.kr E-mail: yoshihiko.yamada@nao.ac.jp E-mail: monodera@phys.ethz.ch

    2012-11-10

    We present a spectroscopic analysis of the metallicities, ages, and alpha-elements of the globular clusters (GCs) in the giant elliptical galaxy (gE) NGC 4636 in the Virgo Cluster. Line indices of the GCs are measured from the integrated spectra obtained with Faint Object Camera and Spectrograph on the Subaru 8.2 m Telescope. We derive [Fe/H] values of 59 GCs based on the Brodie and Huchra method, and [Z/H], age, and [{alpha}/Fe] values of 33 GCs from the comparison of the Lick line indices with single stellar population models. The metallicity distribution of NGC 4636 GCs shows a hint of a bimodality with two peaks at [Fe/H] = -1.23({sigma} = 0.32) and -0.35({sigma} = 0.19). The age spread is large from 2 Gyr to 15 Gyr and the fraction of young GCs with age <5 Gyr is about 27%. The [{alpha}/Fe] of the GCs shows a broad distribution with a mean value [{alpha}/Fe] Almost-Equal-To 0.14 dex. The dependence of these chemical properties on the galactocentric radius is weak. We also derive the metallicities, ages, and [{alpha}/Fe] values for the GCs in other nearby gEs (M87, M49, M60, NGC 5128, NGC 1399, and NGC 1407) from the line index data in the literature using the same methods as used for NGC 4636 GCs. The metallicity distribution of GCs in the combined sample of seven gEs including NGC 4636 is found to be bimodal, supported by the KMM test with a significance level of >99.9%. All these gEs harbor some young GCs with ages less than 5 Gyr. The mean age of the metal-rich GCs ([Fe/H] >-0.9) is about 3 Gyr younger than that of the metal-poor GCs. The mean value of [{alpha}/Fe] of the gE GCs is smaller than that of the Milky Way GCs. We discuss these results in the context of GC formation in gEs.

  13. Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR

    PubMed Central

    Lee, Sang-Won; Berger, Scott J.; Martinović, Suzana; Paša-Tolić, Ljiljana; Anderson, Gordon A.; Shen, Yufeng; Zhao, Rui; Smith, Richard D.

    2002-01-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry coupled with capillary reverse-phase liquid chromatography was used to characterize intact proteins from the large subunit of the yeast ribosome. High mass measurement accuracy, achieved by “mass locking” with an internal standard from a dual electrospray ionization source, allowed identification of ribosomal proteins. Analyses of the intact proteins revealed information on cotranslational and posttranslational modifications of the ribosomal proteins that included loss of the initiating methionine, acetylation, methylation, and proteolytic maturation. High-resolution separations permitted differentiation of protein isoforms having high structural similarity as well as proteins from their modified forms, facilitating unequivocal assignments. The study identified 42 of the 43 core large ribosomal subunit proteins and 58 (of 64 possible) core large subunit protein isoforms having unique masses in a single analysis. These results demonstrate the basis for the high-throughput analyses of complex mixtures of intact proteins, which we believe will be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations. PMID:11983894

  14. Globular Cluster Streams as Galactic High-Precision Scales

    NASA Astrophysics Data System (ADS)

    Küpper, Andreas H. W.; Balbinot, Eduardo; Bonaca, Ana; Johnston, Kathryn V.; Hogg, David W.; Kroupa, Pavel; Santiago, Basilio X.

    2016-08-01

    Tidal streams of globular clusters are ideal tracers of the Galactic gravitational potential. Compared to the few known, complex and diffuse dwarf-galaxy streams, they are kinematically cold, have thin morphologies and are abundant in the halo of the Milky Way. Their coldness and thinness in combination with potential epicyclic substructure in the vicinity of the stream progenitor turns them into high-precision scales. With the example of Palomar 5, we demonstrate how modeling of a globular cluster stream allows us to simultaneously measure the properties of the disrupting globular cluster, its orbital motion, and the gravitational potential of the Milky Way.

  15. BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures

    NASA Astrophysics Data System (ADS)

    Sarti, E.; Zamuner, S.; Cossio, P.; Laio, A.; Seno, F.; Trovato, A.

    2013-12-01

    In protein structure prediction it is of crucial importance, especially at the refinement stage, to score efficiently large sets of models by selecting the ones that are closest to the native state. We here present a new computational tool, BACHSCORE, that allows its users to rank different structural models of the same protein according to their quality, evaluated by using the BACH++ (Bayesian Analysis Conformation Hunt) scoring function. The original BACH statistical potential was already shown to discriminate with very good reliability the protein native state in large sets of misfolded models of the same protein. BACH++ features a novel upgrade in the solvation potential of the scoring function, now computed by adapting the LCPO (Linear Combination of Pairwise Orbitals) algorithm. This change further enhances the already good performance of the scoring function. BACHSCORE can be accessed directly through the web server: bachserver.pd.infn.it. Catalogue identifier: AEQD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQD_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 130159 No. of bytes in distributed program, including test data, etc.: 24 687 455 Distribution format: tar.gz Programming language: C++. Computer: Any computer capable of running an executable produced by a g++ compiler (4.6.3 version). Operating system: Linux, Unix OS-es. RAM: 1 073 741 824 bytes Classification: 3. Nature of problem: Evaluate the quality of a protein structural model, taking into account the possible “a priori” knowledge of a reference primary sequence that may be different from the amino-acid sequence of the model; the native protein structure should be recognized as the best model. Solution method: The contact potential scores the occurrence of any given type of residue pair in 5 possible

  16. The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold

    PubMed Central

    Guo, Zhefeng; Eisenberg, David

    2008-01-01

    Numerous human disorders are associated with the formation of protein fibrils. The fibril-forming capacity of a protein has been found in recent studies to be determined by a short segment of residues that forms a dual β-sheet, called a steric zipper, in the spine of the fibril. The question arises as to whether a fibril-forming segment, when inserted within the sequence of a globular protein, will invariably cause the protein to form fibrils. Here we investigate this question by inserting the known fibril-forming segment NNQQNY into the globular enzyme, T7 endonuclease I. From earlier studies, we know that in its fibril form, NNQQNY is in an extended conformation. We first found that the inserted NNQQNY stimulates fibril formation of T7 endonuclease I in solution. Thus NNQQNY within T7 endonuclease I can exist in an extended conformation, capable of forming the steric zipper in the core of a fibril. We also found that T7 endonuclease I folds into a decamer that does not form fibrils. We determined the structure of the decamer by X-ray crystallography, finding an unusual oligomer without point group symmetry, and finding that the NNQQNY segments within the decamer adopt two twisted conformations, neither is apparently able to fibrillize. We conclude that twisting of fibril forming sequences from the fully extended conformation, imposed by the context of their placement in proteins, can interfere with fibril formation. PMID:18552127

  17. Ultraviolet Spectra of Globular Clusters in Andromeda

    NASA Astrophysics Data System (ADS)

    Peterson, R. C.

    1999-05-01

    As part of a NASA-funded effort with Ben Dorman of Goddard Space Flight Center, I am engaged in calculating spectra from first principles of solar-type stars of a wide range of metallicity. This paper reports on an extension of this work funded by the Hubble Space Telescope archival program, the derivation of fundamental parameters for several globular clusters in Andromeda (M31). Properties of the underlying stellar population are derived by matching archival HST spectra with composite spectra constructed by weighted coaddition of the calculated spectra for stars of appropriate spectral types. Armed with these ab initio calculations, this work explores the degeneracy in age and metallicity in the ultraviolet, and the affect of unknowns such as the relative abundance of light elements versus iron and the possible presence of blue stragglers or blue horizontal branch stars.

  18. Semi-rigidity vs. flexibility in collective variables preselection for metadynamics studies of large proteins

    NASA Astrophysics Data System (ADS)

    Ilieva, N.; Lilkova, E.; Petkov, P.; Litov, L.

    2016-10-01

    In silico investigations of biological molecules rely on the adequate sampling of the systems' conformation space. In the case of large systems, this is a highly non trivial task, which requires the development and refinement of enhanced sampling techniques. Metadynamics — one of these techniques — is based on computation of the free energy of the system as a function of a small set of collective variables (CVs) that are assumed to be able to adequately describe the investigated process. No standard procedures or selection criteria exist for the selection of the optimal set of collective variables. The purpose of our work is to develop a CV selection protocol based on the conformational rigidity of the protein in the most sensitive for the investigated process domains. The structure identification is performed using the spatiotemporal multistage consensus clustering (SMCC), with an appropriate selection of the algorithm parameters.

  19. Lithium-rich Giants in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Kirby, Evan N.; Guhathakurta, Puragra; Zhang, Andrew J.; Hong, Jerry; Guo, Michelle; Guo, Rachel; Cohen, Judith G.; Cunha, Katia

    2016-03-01

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron-Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval. The data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

  20. Expression levels of apoptosis-related proteins predict clinical outcome in anaplastic large cell lymphoma.

    PubMed

    ten Berge, Rosita L; Meijer, Chris J L M; Dukers, Danny F; Kummer, J Alain; Bladergroen, Bellinda A; Vos, Wim; Hack, C Erik; Ossenkoppele, Gert J; Oudejans, Joost J

    2002-06-15

    In vitro studies suggest that resistance to chemotherapy-induced apoptosis might explain poor response to therapy in fatal cases. Actual execution of apoptosis depends on proper functioning of effector caspases, particularly caspase 3, and on the expression levels of apoptosis-regulating proteins, including Bcl-2 and the recently identified granzyme B- specific protease inhibitor 9 (PI9). Thus, high levels of caspase 3 activation should reflect proper functioning of the apoptosis pathways, resulting in chemotherapy-sensitive neoplastic cells and a favorable prognosis. We tested this hypothesis by quantifying numbers of tumor cells positive for active caspase 3, Bcl-2, and PI9, respectively, in pretreatment biopsies of systemic anaplastic large cell lymphoma (ALCL) patients and by comparing these numbers with clinical outcome. Activation of caspase 3 in more than 5% of the tumor cells was strongly correlated with a highly favorable outcome. High numbers of Bcl-2- and PI9-positive tumor cells were found to predict unfavorable prognosis. This prognostic effect was strongly related to anaplastic lymphoma kinase (ALK) status: ALK-positive ALCL had significantly higher levels of active caspase 3, while high expression of the antiapoptotic proteins Bcl-2 and PI9 was almost completely restricted to ALK-negative cases. In conclusion, high numbers of active caspase 3-positive tumor cells predict a highly favorable prognosis in systemic ALCL patients. Poor prognosis is strongly related to high numbers of Bcl-2- and PI9-positive neoplastic cells. These data support the notion that a favorable response to chemotherapy depends on an intact apoptosis cascade. Moreover, these data indicate that differences in prognosis between ALK-positive and ALK-negative ALCL might be explained by differences in expression of apoptosis-inhibiting proteins.

  1. HLA-G and MHC Class II Protein Expression in Diffuse Large B-Cell Lymphoma.

    PubMed

    Jesionek-Kupnicka, Dorota; Bojo, Marcin; Prochorec-Sobieszek, Monika; Szumera-Ciećkiewicz, Anna; Jabłońska, Joanna; Kalinka-Warzocha, Ewa; Kordek, Radzisław; Młynarski, Wojciech; Robak, Tadeusz; Warzocha, Krzysztof; Lech-Maranda, Ewa

    2016-06-01

    The expression of human leukocyte antigen-G (HLA-G) and HLA class II protein was studied by immunohistochemical staining of lymph nodes from 148 patients with diffuse large B-cell lymphoma (DLBCL) and related to the clinical course of the disease. Negative HLA-G expression was associated with a lower probability of achieving a complete remission (p = 0.04). Patients with negative HLA-G expression tended towards a lower 3-year overall survival (OS) rate compared to those with positive expression of HLA-G (p = 0.08). When restricting the analysis to patients receiving chemotherapy with rituximab, the estimated 3-year OS rate of patients with positive HLA-G expression was 73.3 % compared with 47.5 % (p = 0.03) in those with negative expression. Patients with negative HLA class II expression presented a lower 3-year OS rate compared to subjects with positive expression (p = 0.04). The loss of HLA class II expression (p = 0.05) and belonging to the intermediate high/high IPI risk group (p = 0.001) independently increased the risk of death. HLA class II expression also retained its prognostic value in patients receiving rituximab; the 3-year OS rate was 65.3 % in patients with positive HLA class II expression versus 29.6 % (p = 0.04) in subjects that had loss of HLA class II expression. To our knowledge, for the first time, the expression of HLA-G protein in DLBCL and its association with the clinical course of the disease was demonstrated. Moreover, the link between losing HLA class II protein expression and poor survival of patients treated with immunochemotherapy was confirmed.

  2. Characterizing detergent mediated reconstitution of viral protein M2 in large unilamellar vesicles

    NASA Astrophysics Data System (ADS)

    Freyre, Mariel; Grossman, Carl; Crouch, Catherine; Howard, Kathleen

    2015-03-01

    Influenza M2 is a model membrane protein whose function is to induce curvature and vesicle formation in the process of viral infection. To study embedded M2 in synthetic phospholipid vesicles (large unilamellar vesicles or LUVs), a concentration of detergent and buffer is optimized to balance protein solubility, proteolipid concentration, and LUV stability. Adding detergent also causes the LUVs to partially disassemble and form micelles, which warrants detergent removal to restore LUV integrity. We explore methods of measuring the coexistence of detergent micelles and LUVs to track the different phases of the system as detergent is removed. A combination of Fluorescence Correlation Spectroscopy, Dynamic Light Scattering, and chemical analysis are used to measure the properties of this system. With detergent/LUV number densities as high as 5 we find coexistence of micelles and LUVs at 50% to 60%. As the detergent is removed, the micelle concentration drops to lower than 30% while detergent levels drop to nearly zero. These results may indicate a polydispersed LUV size distribution after detergent mediated reconstitution. Supported by HHMI and Swarthmore College.

  3. Artificial membrane-binding proteins stimulate oxygenation of stem cells during engineering of large cartilage tissue

    PubMed Central

    Armstrong, James P. K.; Shakur, Rameen; Horne, Joseph P.; Dickinson, Sally C.; Armstrong, Craig T.; Lau, Katherine; Kadiwala, Juned; Lowe, Robert; Seddon, Annela; Mann, Stephen; Anderson, J. L. Ross; Perriman, Adam W.; Hollander, Anthony P.

    2015-01-01

    Restricted oxygen diffusion can result in central cell necrosis in engineered tissue, a problem that is exacerbated when engineering large tissue constructs for clinical application. Here we show that pre-treating human mesenchymal stem cells (hMSCs) with synthetic membrane-active myoglobin-polymer–surfactant complexes can provide a reservoir of oxygen capable of alleviating necrosis at the centre of hyaline cartilage. This is achieved through the development of a new cell functionalization methodology based on polymer–surfactant conjugation, which allows the delivery of functional proteins to the hMSC membrane. This new approach circumvents the need for cell surface engineering using protein chimerization or genetic transfection, and we demonstrate that the surface-modified hMSCs retain their ability to proliferate and to undergo multilineage differentiation. The functionalization technology is facile, versatile and non-disruptive, and in addition to tissue oxygenation, it should have far-reaching application in a host of tissue engineering and cell-based therapies. PMID:26080734

  4. Artificial membrane-binding proteins stimulate oxygenation of stem cells during engineering of large cartilage tissue

    NASA Astrophysics Data System (ADS)

    Armstrong, James P. K.; Shakur, Rameen; Horne, Joseph P.; Dickinson, Sally C.; Armstrong, Craig T.; Lau, Katherine; Kadiwala, Juned; Lowe, Robert; Seddon, Annela; Mann, Stephen; Anderson, J. L. Ross; Perriman, Adam W.; Hollander, Anthony P.

    2015-06-01

    Restricted oxygen diffusion can result in central cell necrosis in engineered tissue, a problem that is exacerbated when engineering large tissue constructs for clinical application. Here we show that pre-treating human mesenchymal stem cells (hMSCs) with synthetic membrane-active myoglobin-polymer-surfactant complexes can provide a reservoir of oxygen capable of alleviating necrosis at the centre of hyaline cartilage. This is achieved through the development of a new cell functionalization methodology based on polymer-surfactant conjugation, which allows the delivery of functional proteins to the hMSC membrane. This new approach circumvents the need for cell surface engineering using protein chimerization or genetic transfection, and we demonstrate that the surface-modified hMSCs retain their ability to proliferate and to undergo multilineage differentiation. The functionalization technology is facile, versatile and non-disruptive, and in addition to tissue oxygenation, it should have far-reaching application in a host of tissue engineering and cell-based therapies.

  5. Survey of large protein complexes D. vulgaris reveals great structural diversity

    SciTech Connect

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  6. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity

    PubMed Central

    Nikolaev, L.G; Akopov, S.B; Didych, D.A; Sverdlov, E.D

    2009-01-01

    The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s). PMID:20119526

  7. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity.

    PubMed

    Nikolaev, L G; Akopov, S B; Didych, D A; Sverdlov, E D

    2009-08-01

    The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s). PMID:20119526

  8. Large Variation in Detection of Histidine-Rich Protein 2 in Plasmodium falciparum Isolates from Colombia

    PubMed Central

    Pava, Zuleima; Echeverry, Diego F.; Díaz, Gustavo; Murillo, Claribel

    2010-01-01

    Most rapid diagnostic tests (RDTs) available use histidine-rich protein 2 (HRP2) as a target. However, it has been reported that sequence variations of this protein affects its sensitivity. Currently, there is insufficient evidence for HRP2 variability in Plasmodium falciparum isolates from Colombia and its relationship with RDT performance. To determine possible geographic differences and their effects on the performance of RDTs, 22 blood samples from patients with P. falciparum malaria from Tumaco and Buenaventura, Colombia were assessed by measurement of HRP2 concentration by an HRP2 enzyme-linked immunosorbent assay, RDTs, and thick blood smear. Statistical analysis showed an association between RDT performance and HRP2 concentrations. No significant difference was found between locations. A large variation of antigen concentration in samples was found at same parasitemia. In contrast to previously reports, there was no correlation between initial parasitemia and HRP2 concentration. Our results indicate that antigen quantity should be studied more carefully because the sensitivity of the RDT is affected more by antigen concentration than by parasitemia. PMID:20889875

  9. Uncovered: Progenitors of globular clusters showing off their multiple stellar populations

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Li, Chengyuan; Deng, Licai; Geller, Aaron M.; Xin, Yu; Hu, Yi; Faucher-Giguere, Claude-Andre

    2016-01-01

    Stars in star clusters are thought to form in a single burst from a common progenitor cloud of molecular gas, resulting in so-called simple stellar populations. However, old, massive globular clusters—with ages greater than 10 billion years—often host multiple stellar populations, indicating that more than one star-forming event may have occurred during their lifetimes. The most popular scenario for their formation invokes colliding stellar winds from late-stage, asymptotic-giant-branch stars. If this were correct, the initial globular cluster masses should be at least 10 times more massive than their current masses of typically a few x 105 Msun. However, large populations of clusters with masses greater than a few x 106 Msun are not found in the local Universe. Here we present Hubble Space Telescope observations of three 1-2 billion-year-old, massive star clusters in the Magellanic Clouds which show unequivocal evidence of burst-like star-formation activity that occurred a few x 108 years after their initial formation era. The spatial distributions of the younger stellar generations suggest that they may have originated from ambient gas clouds accreted by the clusters while orbiting in the disks of their host galaxies rather than from colliding stellar winds. Simple models imply that such clusters could indeed accrete sufficient gas reservoirs to form these stars. This may eventually give rise to the appearance of multiple stellar populations in globular clusters.

  10. Using globular clusters to test gravity in the weak acceleration regime: NGC 6171

    NASA Astrophysics Data System (ADS)

    Scarpa, Riccardo; Marconi, Gianni; Gilmozzi, Roberto

    2004-12-01

    As part of an ongoing program to test Newton’s law of gravity in the low acceleration regime using globular clusters, we present here new results obtained for NGC 6171. Combining VLT spectra for 107 stars with data from the literature, we were able to trace the velocity dispersion profile up to 16 pc from the cluster center, probing accelerations of gravity down to 3.5x10-9 cm s-2 . The velocity dispersion is found to remain constant at large radii (with an asymptotic values of 2.7 km s-1 ) rather than follow the Keplerian falloff. Similar results were previously found for the globular clusters ω Centauri and M15. We have now studied three clusters and all three have been found to have a flat dispersion profile beyond the radius where their internal acceleration of gravity is a0 1.2x10-8 cm s-2 . Whether this indicates a failure of Newtonian dynamics or some more conventional dynamical effect (e.g., tidal heating) is still unclear. However, the similarities emerging between globular clusters and elliptical galaxies seem to favor the first of the two possibilities.

  11. Globular Clusters as a Test for Gravity in the Weak Acceleration Regime

    NASA Astrophysics Data System (ADS)

    Scarpa, Riccardo; Marconi, Gianni; Gilmozzi, Roberto

    2006-03-01

    Non-baryonic Dark Matter (DM) appears in galaxies and other cosmic structures when and only when the acceleration of gravity, as computed considering only baryons, goes below a well defined value a0 = 1.2 × 10-8 cm s-2. This fact is extremely important and suggestive of the possibility of a breakdown of Newton's law of gravity (or inertia) below a0. It is therefore important to verify whether Newton's law of gravity holds in this regime of accelerations. In order to do this, one has to study the dynamics of objects that do not contain significant amounts of DM and therefore should follow Newton's prediction for whatever small accelerations. Globular clusters are believed, even by strong supporters of DM, to contain negligible amounts of DM and therefore are ideal for testing Newtonian dynamics in the low acceleration limit. Here, we discuss the status of an ongoing program aimed to do this test. Compared to other studies of globular clsuters, the novelty is that we trace the velocity dispersion profile of globular clusters far enough from the center to probe gravitational accelerations well below a0. In all three clusters studied so far the velocity dispersion is found to remain constant at large radii rather than follow the Keplerian falloff. On average, the flattening occurs at the radius where the cluster internal acceleration of gravity is 1.8 +/- 0.4 × 10-8 cm s-2, fully consistent with MOND predictions.

  12. A DYING STAR IN GLOBULAR CLUSTER

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A DYING STAR IN GLOBULAR CLUSTER M15 The globular cluster Messier 15 is shown in this color image obtained with the NASA Hubble Space Telescope's Wide Field Planetary Camera 2 (WFPC2). Lying some 40,000 light-years from Earth in the direction of the constellation Pegasus, M15 is one of nearly 150 known globular clusters that form a vast halo surrounding our Milky Way galaxy. Each of these clusters is a spherical association of hundreds of thousands of ancient stars. The image, prepared by the Hubble Heritage team, attempts to show the stars in M15 in their true colors. The brightest cluster stars are red giants, with an orange color due to surface temperatures lower than our Sun's. Most of the fainter stars are hotter, giving them a bluish-white color. If we lived in the core of M15, our sky would blaze with tens of thousands of brilliant stars both day and night! Nestled among the myriads of stars visible in the Hubble image is an astronomical oddity. The pinkish object to the upper left of the cluster's core is a gas cloud surrounding a dying star. Known as Kuestner 648, this was the first planetary nebula to be identified in a globular cluster. In 1928, F. G. Pease, working at the 100-inch telescope of California's Mount Wilson Observatory, photographed the spectrum of K 648 and discovered the telltale bright emission of a nebular gas cloud rather than a normal star. In the ensuing 70 years, only three more planetary nebulae have been discovered in globular clusters. The stars in M15 and other globular clusters are estimated to be about 12 billion years old. They were among the first generations of stars to form in the Milky Way. Our Sun, by comparison, is a youthful 4.6 billion years old. As a star like the Sun ages, it exhausts the hydrogen that fuels its nuclear fusion, and increases in size to become a red giant. Then it ejects its outer layers into space, producing a planetary nebula. The remnant star at the center of the nebula gradually dies away as a

  13. A DYING STAR IN GLOBULAR CLUSTER

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A DYING STAR IN GLOBULAR CLUSTER M15 The globular cluster Messier 15 is shown in this color image obtained with the NASA Hubble Space Telescope's Wide Field Planetary Camera 2 (WFPC2). Lying some 40,000 light-years from Earth in the direction of the constellation Pegasus, M15 is one of nearly 150 known globular clusters that form a vast halo surrounding our Milky Way galaxy. Each of these clusters is a spherical association of hundreds of thousands of ancient stars. The image, prepared by the Hubble Heritage team, attempts to show the stars in M15 in their true colors. The brightest cluster stars are red giants, with an orange color due to surface temperatures lower than our Sun's. Most of the fainter stars are hotter, giving them a bluish-white color. If we lived in the core of M15, our sky would blaze with tens of thousands of brilliant stars both day and night! Nestled among the myriads of stars visible in the Hubble image is an astronomical oddity. The pinkish object to the upper left of the cluster's core is a gas cloud surrounding a dying star. Known as Kuestner 648, this was the first planetary nebula to be identified in a globular cluster. In 1928, F. G. Pease, working at the 100-inch telescope of California's Mount Wilson Observatory, photographed the spectrum of K 648 and discovered the telltale bright emission of a nebular gas cloud rather than a normal star. In the ensuing 70 years, only three more planetary nebulae have been discovered in globular clusters. The stars in M15 and other globular clusters are estimated to be about 12 billion years old. They were among the first generations of stars to form in the Milky Way. Our Sun, by comparison, is a youthful 4.6 billion years old. As a star like the Sun ages, it exhausts the hydrogen that fuels its nuclear fusion, and increases in size to become a red giant. Then it ejects its outer layers into space, producing a planetary nebula. The remnant star at the center of the nebula gradually dies away as a

  14. Sucralose Destabilization of Protein Structure.

    PubMed

    Chen, Lee; Shukla, Nimesh; Cho, Inha; Cohn, Erin; Taylor, Erika A; Othon, Christina M

    2015-04-16

    Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion. PMID:26263149

  15. Measuring consistent masses for 25 Milky Way globular clusters

    SciTech Connect

    Kimmig, Brian; Seth, Anil; Ivans, Inese I.; Anderton, Tim; Gregersen, Dylan; Strader, Jay; Caldwell, Nelson

    2015-02-01

    We present central velocity dispersions, masses, mass-to-light ratios (M/Ls ), and rotation strengths for 25 Galactic globular clusters (GCs). We derive radial velocities of 1951 stars in 12 GCs from single order spectra taken with Hectochelle on the MMT telescope. To this sample we add an analysis of available archival data of individual stars. For the full set of data we fit King models to derive consistent dynamical parameters for the clusters. We find good agreement between single-mass King models and the observed radial dispersion profiles. The large, uniform sample of dynamical masses we derive enables us to examine trends of M/L with cluster mass and metallicity. The overall values of M/L and the trends with mass and metallicity are consistent with existing measurements from a large sample of M31 clusters. This includes a clear trend of increasing M/L with cluster mass and lower than expected M/Ls for the metal-rich clusters. We find no clear trend of increasing rotation with increasing cluster metallicity suggested in previous work.

  16. A general path for large-scale solubilization of cellular proteins: From membrane receptors to multiprotein complexes

    PubMed Central

    Pullara, Filippo; Guerrero-Santoro, Jennifer; Calero, Monica; Zhang, Qiangmin; Peng, Ye; Spåhr, Henrik; Kornberg, Guy L.; Cusimano, Antonella; Stevenson, Hilary P.; Santamaria-Suarez, Hugo; Reynolds, Shelley L.; Brown, Ian S.; Monga, Satdarshan P.S.; Van Houten, Bennett; Rapić-Otrin, Vesna; Calero, Guillermo; Levine, Arthur S.

    2014-01-01

    Expression of recombinant proteins in bacterial or eukaryotic systems often results in aggregation rendering them unavailable for biochemical or structural studies. Protein aggregation is a costly problem for biomedical research. It forces research laboratories and the biomedical industry to search for alternative, more soluble, non-human proteins and limits the number of potential “druggable” targets. In this study we present a highly reproducible protocol that introduces the systematic use of an extensive number of detergents to solubilize aggregated proteins expressed in bacterial and eukaryotic systems. We validate the usefulness of this protocol by solubilizing traditionally difficult human protein targets to milligram quantities and confirm their biological activity. We use this method to solubilize monomeric or multimeric components of multi-protein complexes and demonstrate its efficacy to reconstitute large cellular machines. This protocol works equally well on cytosolic, nuclear and membrane proteins and can be easily adapted to a high throughput format. PMID:23137940

  17. W UMA-Type Binary Stars in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Rucinski, Slavek M.

    2000-07-01

    A sample of 86 contact binary systems in 14 globular clusters with available color index data in B-V or in V-I has been analyzed. A large fraction of all systems (at least one-third) are numerous foreground Galactic disk projections over long lines of sight to the clusters. Since the selection of the cluster members has been based on the MV(logP,color) calibrations, the matter of a metallicity correction required particular attention with the result that such a correction is apparently not needed at the present level of accuracy. Analysis of the color-magnitude and period-color relations shows that globular cluster members have different properties from the Galactic disk contact systems: They are underluminous mainly because of the smaller sizes and, consequently, have shorter orbital periods; the color-index effect of the diminished blanketing is relatively less important, especially for V-I. Among the class 1 members (deviations in MV smaller than 0.5 mag), the most common are blue straggler (BS) systems. The variability amplitudes for the BS systems show a significantly different distribution from that for systems below the turn-off point (TOP): The BS systems in the sample have only small amplitudes (which may be an indication of small mass ratios), while the distribution for the systems below the TOP is peculiar in containing only large-amplitude systems. This difference may be linked to the relatively small number of the detected main-sequence contact systems below the TOP as resulting from an observational selection effect due to the rapidly increasing measurement difficulties below the TOP. As a consequence, efforts at determining the frequency of occurrence of the contact systems below the TOP have been judged to be premature. The frequency among the BS stars could be moderately well established at about 45+/-10 BS stars per one contact BS binary; thus, contact binaries are about 3 times more common among the BS stars than among the disk population dwarfs

  18. THE ACCRETION OF DWARF GALAXIES AND THEIR GLOBULAR CLUSTER SYSTEMS

    SciTech Connect

    Masters, Craig E.; Ashman, Keith M. E-mail: ashmank@umkc.ed

    2010-12-10

    The question of where the low-metallicity globular clusters in early-type galaxies came from has profound implications for the formation of those galaxies. Our work supports the idea that the metal-poor globular cluster systems of giant early-type galaxies formed in dwarf galaxies that have been subsumed by the giants. To support this hypothesis, two linear relations, one involving globular cluster metallicity versus host galaxy luminosity and one involving metallicity versus velocity dispersion were studied. Tentatively, these relations show that the bright ellipticals do not obey the same trend as the dwarfs, suggesting that the low-metallicity globular clusters did not form within their parent bright ellipticals.

  19. Globular clusters in the halo of M31

    SciTech Connect

    Racine, R. Canada-France-Hawaii Telescope Corp., Kamuela, HI )

    1991-03-01

    The CFHT was used to obtain high-resolution CCD images of 82 cluster candidates in the halo of M31. These data, combined with radial velocities which cover an additional 27 candidates, are used to compile a catalog of 51 bona fide M31 halo globulars. The other candidates are found to be background galaxies (54) and field stars (4). The cluster sample appears to be incomplete for V greater than 18. The projected distribution of globulars follows an 1/r-squared law for r(kpc) between values of 6 and 22 and then drops faster, suggesting a cutoff at about 40 kpc. These trends are similar to those for globular clusters in the Milky Way halo. The total populaton of globulars in M31 is estimated to be larger than in the Milky Way by a factor of 1.8 + or - 0.3. 30 refs.

  20. MUSE crowded field 3D spectroscopy of over 12 000 stars in the globular cluster NGC 6397. I. The first comprehensive HRD of a globular cluster

    NASA Astrophysics Data System (ADS)

    Husser, Tim-Oliver; Kamann, Sebastian; Dreizler, Stefan; Wendt, Martin; Wulff, Nina; Bacon, Roland; Wisotzki, Lutz; Brinchmann, Jarle; Weilbacher, Peter M.; Roth, Martin M.; Monreal-Ibero, Ana

    2016-04-01

    Aims: We demonstrate the high multiplex advantage of crowded field 3D spectroscopy with the new integral field spectrograph MUSE by means of a spectroscopic analysis of more than 12 000 individual stars in the globular cluster NGC 6397. Methods: The stars are deblended with a point spread function fitting technique, using a photometric reference catalogue from HST as prior, including relative positions and brightnesses. This catalogue is also used for a first analysis of the extracted spectra, followed by an automatic in-depth analysis via a full-spectrum fitting method based on a large grid of PHOENIX spectra. Results: We analysed the largest sample so far available for a single globular cluster of 18 932 spectra from 12 307 stars in NGC 6397. We derived a mean radial velocity of vrad = 17.84 ± 0.07 km s-1 and a mean metallicity of [Fe/H] = -2.120 ± 0.002, with the latter seemingly varying with temperature for stars on the red giant branch (RGB). We determine Teff and [Fe/H] from the spectra, and log g from HST photometry. This is the first very comprehensive Hertzsprung-Russell diagram (HRD) for a globular cluster based on the analysis of several thousands of stellar spectra, ranging from the main sequence to the tip of the RGB. Furthermore, two interesting objects were identified; one is a post-AGB star and the other is a possible millisecond-pulsar companion. Data products are available at http://muse-vlt.eu/scienceBased on observations obtained at the Very Large Telescope (VLT) of the European Southern Observatory, Paranal, Chile (ESO Programme ID 60.A-9100(C)).

  1. Biophysics of protein evolution and evolutionary protein biophysics

    PubMed Central

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  2. Small-Scale Screening to Large-Scale Over-Expression of Human Membrane Proteins for Structural Studies.

    PubMed

    Chaudhary, Sarika; Saha, Sukanya; Thamminana, Sobrahani; Stroud, Robert M

    2016-01-01

    Membrane protein structural studies are frequently hampered by poor expression. The low natural abundance of these proteins implies a need for utilizing different heterologous expression systems. E. coli and yeast are commonly used expression systems due to rapid cell growth at high cell density, economical production, and ease of manipulation. Here we report a simplified, systematically developed robust strategy from small-scale screening to large-scale over-expression of human integral membrane proteins in the mammalian expression system for structural studies. This methodology streamlines small-scale screening of several different constructs utilizing fluorescence size-exclusion chromatography (FSEC) towards optimization of buffer, additives, and detergents for achieving stability and homogeneity. This is followed by the generation of stable clonal cell lines expressing desired constructs, and lastly large-scale expression for crystallization. These techniques are designed to rapidly advance the structural studies of eukaryotic integral membrane proteins including that of human membrane proteins. PMID:27485338

  3. Binding of chara Myosin globular tail domain to phospholipid vesicles.

    PubMed

    Nunokawa, Shun-Ya; Anan, Hiromi; Shimada, Kiyo; Hachikubo, You; Kashiyama, Taku; Ito, Kohji; Yamamoto, Keiichi

    2007-11-01

    Binding of Chara myosin globular tail domain to phospholipid vesicles was investigated quantitatively. It was found that the globular tail domain binds to vesicles made from acidic phospholipids but not to those made from neutral phospholipids. This binding was weakened at high KCl concentration, suggesting that the binding is electrostatic by nature. The dissociation constant for the binding of the globular tail domain to 20% phosphatidylserine vesicles (similar to endoplasmic reticulum in acidic phospholipid contents) at 150 mM KCl was 273 nM. The free energy change due to this binding calculated from the dissociation constant was -37.3 kJ mol(-1). Thus the bond between the globular tail domain and membrane phospholipids would not be broken when the motor domain of Chara myosin moves along the actin filament using the energy of ATP hydrolysis (DeltaG degrees ' = -30.5 kJ mol(-1)). Our results suggested that direct binding of Chara myosin to the endoplasmic reticulum membrane through the globular tail domain could work satisfactorily in Chara cytoplasmic streaming. We also suggest a possible regulatory mechanism of cytoplasmic streaming including phosphorylation-dependent dissociation of the globular tail domain from the endoplasmic reticulum membrane.

  4. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis.

    PubMed

    Sharff, A J; Rodseth, L E; Spurlino, J C; Quiocho, F A

    1992-11-10

    The periplasmic maltodextrin binding protein of Escherichia coli serves as an initial receptor for the active transport of and chemotaxis toward maltooligosaccharides. The three-dimensional structure of the binding protein complexed with maltose has been previously reported [Spurlino, J. C., Lu, G.-Y., & Quiocho, F. A. (1991) J. Biol. Chem. 266, 5202-5219]. Here we report the structure of the unliganded form of the binding protein refined to 1.8-A resolution. This structure, combined with that for the liganded form, provides the first crystallographic evidence that a major ligand-induced conformational change occurs in a periplasmic binding protein. The unliganded structure shows a rigid-body "hinge-bending" between the two globular domains by approximately 35 degrees, relative to the maltose-bound structure, opening the sugar binding site groove located between the two domains. In addition, there is an 8 degrees twist of one domain relative to the other domain. The conformational changes observed between this structure and the maltose-bound structure are consistent with current models of maltose/maltodextrin transport and maltose chemotaxis and solidify a mechanism for receptor differentiation between the ligand-free and ligand-bound forms in signal transduction.

  5. The incidence of binaries in globular cluster stellar populations

    NASA Astrophysics Data System (ADS)

    Lucatello, S.; Sollima, A.; Gratton, R.; Vesperini, E.; D'Orazi, V.; Carretta, E.; Bragaglia, A.

    2015-12-01

    Binary fraction and orbital characteristics provide indications on the conditions of star formation, as they shed light on the environment they were born in. Multiple systems are more common in low density environments than in higher density environments. In the current debate about the formation of globular clusters and their multiple populations, studying the binary incidence in the populations they host offers a crucial piece of information on the environment of their birth and their subsequent dynamical evolution. Through a multiyear observational campaign using FLAMES at VLT, we monitored the radial velocity of 968 red-giant-branch stars located around the half-light radii in a sample of ten Galactic globular clusters. We found a total of 21 radial velocity variables identified as bona fide binary stars, for a binary fraction of 2.2% ± 0.5%. When separating the sample into first generation and second generation stars, we find a binary fraction of 4.9% ± 1.3% and 1.2% ± 0.4%, respectively. Through simulations that take possible sources of bias into account in detecting radial velocity variations in the two populations, we show that the difference is significant and only marginally affected by these effects. This kind of different binary fraction strongly suggests different conditions in the environment of formation and evolution of first and second generations stars, with the latter being born in a much denser environment. Our result hence strongly supports the idea that the second generation forms in a dense subsystem at the center of the loosely distributed first generation, where (loose) binaries are efficiently destroyed. Based on data obtained with the Very Large Telescope at the European Southern Observatory, programs: 073.D-0100, 073.D-0211 and 083.D-0208.Full Tables 1, 3, and table of the individual radial velocities are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc

  6. Large-scale analysis of macromolecular crowding effects on protein aggregation using a reconstituted cell-free translation system

    PubMed Central

    Niwa, Tatsuya; Sugimoto, Ryota; Watanabe, Lisa; Nakamura, Shugo; Ueda, Takuya; Taguchi, Hideki

    2015-01-01

    Proteins must fold into their native structures in the crowded cellular environment, to perform their functions. Although such macromolecular crowding has been considered to affect the folding properties of proteins, large-scale experimental data have so far been lacking. Here, we individually translated 142 Escherichia coli cytoplasmic proteins using a reconstituted cell-free translation system in the presence of macromolecular crowding reagents (MCRs), Ficoll 70 or dextran 70, and evaluated the aggregation propensities of 142 proteins. The results showed that the MCR effects varied depending on the proteins, although the degree of these effects was modest. Statistical analyses suggested that structural parameters were involved in the effects of the MCRs. Our dataset provides a valuable resource to understand protein folding and aggregation inside cells. PMID:26500644

  7. istar: a web platform for large-scale protein-ligand docking.

    PubMed

    Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J; Wong, Man-Hon

    2014-01-01

    Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

  8. Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins

    NASA Astrophysics Data System (ADS)

    Bondalapati, Somasekhar; Jbara, Muhammad; Brik, Ashraf

    2016-05-01

    Methods to prepare proteins that include a specific modification at a desired position are essential for understanding their cellular functions and physical properties in living systems. Chemical protein synthesis, which relies on the chemoselective ligation of unprotected peptides, enables the preparation of modified proteins that are not easily fabricated by other methods. In contrast to recombinant approaches, chemical synthesis can be used to prepare protein analogues such as D-proteins, which are useful in protein structure determination and the discovery of novel therapeutics. Post-translationally modifying proteins is another example where chemical protein synthesis proved itself as a powerful approach for preparing samples with high homogeneity and in workable quantities. In this Review, we discuss the basic principles of the field, focusing on novel chemoselective peptide ligation approaches such as native chemical ligation and the recent advances based on this method with a proven record of success in the synthesis of highly important protein targets.

  9. Identification of the p53 protein domain involved in formation of the simian virus 40 large T-antigen-p53 protein complex.

    PubMed Central

    Tan, T H; Wallis, J; Levine, A J

    1986-01-01

    An expression vector utilizing the enhancer and promoter region of the simian virus 40 (SV40) DNA regulating a murine p53 cDNA clone was constructed. The vector produced murine p53 protein in monkey cells identified by five different monoclonal antibodies, three of which were specific for the murine form of p53. The murine p53 produced in monkey cells formed an oligomeric protein complex with the SV40 large tumor antigen. A large number of deletion mutations, in-frame linker insertion mutations, and linker insertion mutations resulting in a frameshift mutation were constructed in the cDNA coding portion of the p53 protein expression vector. The wild-type and mutant p53 cDNA vectors were expressed in monkey cells producing the SV40 large T antigen. The conformation and levels of p53 protein and its ability to form protein complexes with the SV40 T antigen were determined by using five different monoclonal antibodies with quite distinct epitope recognition sites. Insertion mutations between amino acid residues 123 and 215 (of a total of 390 amino acids) eliminated the ability of murine p53 to bind to the SV40 large T antigen. Deletion (at amino acids 11 through 33) and insertion mutations (amino acids 222 through 344) located on either side of this T-antigen-binding protein domain produced a murine p53 protein that bound to the SV40 large T antigen. The same five insertion mutations that failed to bind with the SV40 large T antigen also failed to react with a specific monoclonal antibody, PAb246. In contrast, six additional deletion and insertion mutations that produced p53 protein that did bind with T antigen were each recognized by PAb246. The proposed epitope for PAb246 has been mapped adjacent (amino acids 88 through 109) to the T-antigen-binding domain (amino acids 123 through 215) localized by the mutations mapped in this study. Finally, some insertion mutations that produced a protein that failed to bind to the SV40 T antigen appeared to have an enhanced

  10. Probing the faintest stars in a globular star cluster.

    PubMed

    Richer, Harvey B; Anderson, Jay; Brewer, James; Davis, Saul; Fahlman, Gregory G; Hansen, Brad M S; Hurley, Jarrod; Kalirai, Jasonjot S; King, Ivan R; Reitzel, David; Rich, R Michael; Shara, Michael M; Stetson, Peter B

    2006-08-18

    NGC 6397 is the second closest globular star cluster to the Sun. Using 5 days of time on the Hubble Space Telescope, we have constructed an ultradeep color-magnitude diagram for this cluster. We see a clear truncation in each of its two major stellar sequences. Faint red main-sequence stars run out well above our observational limit and near to the theoretical prediction for the lowest mass stars capable of stable hydrogen burning in their cores. We also see a truncation in the number counts of faint blue stars, namely white dwarfs. This reflects the limit to which the bulk of the white dwarfs can cool over the lifetime of the cluster. There is also a turn toward bluer colors in the least luminous of these objects. This was predicted for the very coolest white dwarfs with hydrogen-rich atmospheres as the formation of H(2) and the resultant collision-induced absorption cause their atmospheres to become largely opaque to infrared radiation.

  11. ROTATION AND MULTIPLE STELLAR POPULATION IN GLOBULAR CLUSTERS

    SciTech Connect

    Bekki, Kenji

    2010-11-20

    We investigate structure and kinematics of the second generation of stars (SG) formed from gaseous ejecta of the first generation of stars (FG) in forming globular clusters (GCs). We consider that SG can be formed from gaseous ejecta from asymptotic giant branch stars of FG with the initial total mass of 10{sup 6} M {sub sun}-10{sup 8} M {sub sun} to explain the present masses of the Galactic GCs. Our three-dimensional hydrodynamical simulations with star formation show that SG formed in the central regions of FG can have a significant amount of rotation (V/{sigma}{approx} 0.8-2.5). The rotational amplitude of SG can depend strongly on the initial kinematics of FG. We thus propose that some GCs composed of FG and SG had a significant amount of rotation when they were formed. We also suggest that although later long-term ({approx}10 Gyr) dynamical evolution of stars can smooth out the initial structural and kinematical differences between FG and SG to a large extent, initial flattened structures and rotational kinematics of SG can be imprinted on shapes and internal rotation of the present GCs. We discuss these results in terms of internal rotation observed in the Galactic GCs.

  12. MAPPING DIFFERENTIAL REDDENING IN THE INNER GALACTIC GLOBULAR CLUSTER SYSTEM

    SciTech Connect

    Alonso-Garcia, Javier; Mateo, Mario; Sen, Bodhisattva; Banerjee, Moulinath; Von Braun, Kaspar E-mail: mmateo@umich.edu E-mail: moulib@umich.edu

    2011-05-15

    A serious limitation in the study of many globular clusters-especially those located near the Galactic center-has been the existence of large and differential extinction by foreground dust. In a series of papers, we intend to map the differential extinction and remove its effects, using a new dereddening technique, in a sample of clusters in the direction of the inner Galaxy, observed using the Magellan 6.5 m telescope and the Hubble Space Telescope. These observations and their analysis will let us produce high-quality color-magnitude diagrams of these poorly studied clusters that will allow us to determine these clusters' relative ages, distances, and chemistry and to address important questions about the formation and the evolution of the inner Galaxy. We also intend to use the maps of the differential extinction to sample and characterize the interstellar medium along the numerous low-latitude lines of sight where the clusters in our sample lie. In this first paper, we describe in detail our dereddening method along with the powerful statistics tools that allow us to apply it, and we show the kind of results that we can expect, applying the method to M62, one of the clusters in our sample. The width of the main sequence and lower red giant branch narrows by a factor of two after applying our dereddening technique, which will significantly help to constrain the age, distance, and metallicity of the cluster.

  13. Probing the faintest stars in a globular star cluster.

    PubMed

    Richer, Harvey B; Anderson, Jay; Brewer, James; Davis, Saul; Fahlman, Gregory G; Hansen, Brad M S; Hurley, Jarrod; Kalirai, Jasonjot S; King, Ivan R; Reitzel, David; Rich, R Michael; Shara, Michael M; Stetson, Peter B

    2006-08-18

    NGC 6397 is the second closest globular star cluster to the Sun. Using 5 days of time on the Hubble Space Telescope, we have constructed an ultradeep color-magnitude diagram for this cluster. We see a clear truncation in each of its two major stellar sequences. Faint red main-sequence stars run out well above our observational limit and near to the theoretical prediction for the lowest mass stars capable of stable hydrogen burning in their cores. We also see a truncation in the number counts of faint blue stars, namely white dwarfs. This reflects the limit to which the bulk of the white dwarfs can cool over the lifetime of the cluster. There is also a turn toward bluer colors in the least luminous of these objects. This was predicted for the very coolest white dwarfs with hydrogen-rich atmospheres as the formation of H(2) and the resultant collision-induced absorption cause their atmospheres to become largely opaque to infrared radiation. PMID:16917054

  14. The X-Ray Globular Cluster Population in NGC 1399

    NASA Technical Reports Server (NTRS)

    Angelini, Lorella; Loewenstein, Michael; Mushotzky, Richard F.; White, Nicholas E. (Technical Monitor)

    2001-01-01

    We report on X-ray sources detected in the Chandra images of the elliptical galaxy NGC 1399 and identified with globular clusters (GCs). The 8'x 8' Chandra image shows that a large fraction of the 2-10 keV X-ray emission is resolved into point sources, with a luminosity threshold of 5 x 10 (exp 37) ergs s-1. These sources are most likely Low Mass X-ray Binaries (LMXBs). More than 70% of the X-ray sources, in a region imaged by Hubble Space Telescope (HST), are located within GCs. Many of these sources have super-Eddington luminosity (for an accreting neutron star) and their average luminosity is higher than the remaining sources. This association suggests that, in giant elliptical galaxies, luminous X-ray binaries preferentially form in GCs. The spectral properties of the GC and non-GC sources are in most cases similar to those of LMXBs in our galaxy. Two of the brightest sources, one of which is in GC, have a much softer spectra as seen in the high state black hole. The "apparent" super-Eddington luminosity in many cases may be due to multiple LMXB systems within individual GC, but with some of the most extreme luminous systems containing massive black holes.

  15. Multipole-storage-assisted dissociation for the characterization of large proteins and simple protein mixtures by ESI-FTICR-MS.

    PubMed

    Pan, Chongle; Hettich, Robert L

    2005-05-15

    In Fourier transform ion cyclotron resonance mass spectrometry, collisionally activated dissociation (CAD) typically is accomplished within the analyzer ion cell. An alternative approach of multipole-storage-assisted dissociation (MSAD) has previously been demonstrated by inducing collisional fragmentation in the external multipole that is usually employed for ion accumulation. To explore the utility of MSAD for interrogating intact proteins and simple protein mixtures in a multiplexed manner, we have investigated the means of controlling the collisional energy and the fragmentation pattern for this experimental approach. With protein samples in the low micromolar concentration range, the two major experimental parameters affecting MSAD in the hexapole region were found to be the dc offset voltage and accumulation time. While low-energy MSAD of intact proteins yields fragment ions similar to sustained off resonance irradiation collision-activated dissociation (SORI-CAD), high-energy MSAD induces sequential fragmentation for intact proteins to yield a rich variety of singly charged ions in the m/z 600-1200 Da region. Each of the seven proteins (Mr range of 8.5-116 kDa) examined in this study exhibited their own characteristic MSAD fragmentation pattern, which could be used as a signature of the presence of a given protein, even in a mixture. In addition, any MSAD fragment can be isolated and dissociated further by SORI-CAD in an MS3-type experiment inside the FTICR analyzer cell. This presents a novel way to interrogate the identities of these fragment ions as well as obtain amino acid sequence tag information that can be used to identify proteins from mixtures.

  16. Analyzing Large-Scale Structural Change in Proteins: Comparison of Principal Component Projection and Sammon Mapping

    SciTech Connect

    Mesentean, Sidonia; Fischer, S.; Smith, Jeremy C

    2006-04-01

    Effective analysis of large-scale conformational transitions in macromolecules requires transforming them into a lower dimensional representation that captures the dominant motions. Herein, we apply and compare two different dimensionality reduction techniques, namely, principal component analysis (PCA), a linear method, and Sammon mapping, which is nonlinear. The two methods are used to analyze four different protein transition pathways of varying complexity, obtained by using either the conjugate peak refinement method or constrained molecular dynamics. For the return-stroke in myosin, both Sammon mapping and PCA show that the conformational change is dominated by a simple rotation of a rigid body. Also, in the case of the T{yields}R transition in hemoglobin, both methods are able to identify the two main quaternary transition events. In contrast, in the cases of the unfolding transition of staphylococcal nuclease or the signaling switch of Ras p21, which are both more complex conformational transitions, only Sammon mapping is able to identify the distinct phases of motion.

  17. HST Snapshot Study of Variable Stars in Globular Clusters: Inner Region of NGC 6441

    NASA Technical Reports Server (NTRS)

    Pritzl, Barton J.; Smith, Horace A.; Stetson, Peter B.; Catelan, Marcio; Sweigart, Allen V.; Layden, Andrew C.; Rich, R. Michael

    2003-01-01

    We present the results of a Hubble Space Telescope snapshot program to survey the inner region of the metal-rich globular cluster NGC 6441 for its variable stars. A total of 57 variable stars was found including 38 RR Lyrae stars, 6 Population II Cepheids, and 12 long period variables. Twenty-four of the RR Lyrae stars and all of the Population II Cepheids were previously undiscovered in ground-based surveys. Of the RR Lyrae stars observed in h s survey, 26 are pulsating in the fundamental mode with a mean period of 0.753 d and 12 are first-overtone mode pulsators with a mean period of 0.365 d. These values match up very well with those found in ground-based surveys. Combining all the available data for NGC 6441, we find mean periods of 0.759 d and 0.375 d for the RRab and RRc stars, respectively. We also find that the RR Lyrae in this survey are located in the same regions of a period-amplitude diagram as those found in ground-based surveys. The overall ratio of RRc to total RR Lyrae is 0.33. Although NGC 6441 is a metal-rich globular cluster and would, on that ground, be expected either to have few RR Lyrae stars, or to be an Oosterhoff type I system, its RR Lyrae more closely resemble those in Oosterhoff type II globular clusters. However, even compared to typical Oosterhoff type II systems, the mean period of its RRab stars is unusually long. We also derived I-band period-luminosity relations for the RR Lyrae stars. Of the six Population II Cepheids, five are of W Virginis type and one is a BL Herculis variable star. This makes NGC 6441, along with NGC 6388, the most metal-rich globular cluster known to contain these types of variable stars. Another variable, V118, may also be a Population II Cepheid given its long period and its separation in magnitude from the RR Lyrae stars. We examine the period-luminosity relation for these Population II Cepheids and compare it to those in other globular clusters and in the Large Magellanic Cloud. We argue that there does

  18. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    PubMed Central

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. PMID:25774711

  19. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins.

    PubMed

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  20. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    NASA Astrophysics Data System (ADS)

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-03-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  1. Large-Scale Identification of Putative Exported Proteins in Candida albicans by Genetic Selection

    PubMed Central

    Monteoliva, L.; López Matas, M.; Gil, C.; Nombela, C.; Pla, J.

    2002-01-01

    In all living organisms, secreted proteins play essential roles in different processes. Of special interest is the construction of the fungal cell wall, since this structure is absent from mammalian cells. The identification of the proteins involved in its biogenesis is therefore a primary goal in antifungal research. To perform a systematic identification of such proteins in Candida albicans, we carried out a genetic screening in which in-frame fusions with an intracellular allele of invertase gene SUC2 of Saccharomyces cerevisiae can be used to select and identify putatively exported proteins in the heterologous host S. cerevisiae. Eighty-three clones were selected, including 11 previously identified genes from C. albicans as well as 41 C. albicans genes that encode proteins homologous to already described proteins from related organisms. They include enzymes involved in cell wall synthesis and protein secretion. We also found membrane receptors and transporters presumably related to the interaction of C. albicans with the environment as well as extracellular enzymes and proteins involved in different morphological transitions. In addition, 11 C. albicans open reading frames (ORFs) identified in this screening encode proteins homologous to unknown or putative proteins, while 5 ORFs encode novel secreted proteins without known homologues in other organisms. This screening procedure therefore not only identifies a set of targets of interest in antifungal research but also provides new clues for understanding the topological locations of many proteins involved in processes relevant to the pathogenicity of this microorganism. PMID:12456000

  2. Absolute Proper Motions of Southern Globular Clusters

    NASA Astrophysics Data System (ADS)

    Dinescu, D. I.; Girard, T. M.; van Altena, W. F.

    1996-05-01

    Our program involves the determination of absolute proper motions with respect to galaxies for a sample of globular clusters situated in the southern sky. The plates cover a 6(deg) x 6(deg) area and are taken with the 51-cm double astrograph at Cesco Observatory in El Leoncito, Argentina. We have developed special methods to deal with the modelling error of the plate transformation and we correct for magnitude equation using the cluster stars. This careful astrometric treatment leads to accuracies of from 0.5 to 1.0 mas/yr for the absolute proper motion of each cluster, depending primarily on the number of measurable cluster stars which in turn is related to the cluster's distance. Space velocities are then derived which, in association with metallicities, provide key information for the formation scenario of the Galaxy, i.e. accretion and/or dissipational collapse. Here we present results for NGC 1851, NGC 6752, NGC 6584, NGC 6362 and NGC 288.

  3. Population Models for Massive Globular Clusters

    NASA Astrophysics Data System (ADS)

    Lee, Young-Wook; Joo, Seok-Joo; Han, Sang-Il; Na, Chongsam; Lim, Dongwook; Roh, Dong-Goo

    2015-03-01

    Increasing number of massive globular clusters (GCs) in the Milky Way are now turned out to host multiple stellar populations having different heavy element abundances enriched by supernovae. Recent observations have further shown that [CNO/Fe] is also enhanced in metal-rich subpopulations in most of these GCs, including ω Cen and M22 (Marino et al. 2011, 2012). In order to reflect this in our population modeling, we have expanded the parameter space of Y 2 isochrones and horizontal-branch (HB) evolutionary tracks to include the cases of normal and enhanced nitrogen abundances ([N/Fe] = 0.0, 0.8, and 1.6). The observed variations in the total CNO content were reproduced by interpolating these nitrogen enhanced stellar models. Our test simulations with varying N and O abundances show that, once the total CNO sum ([CNO/Fe]) is held constant, both N and O have almost identical effects on the HR diagram (see Fig. 1).

  4. Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

    PubMed

    Kapoor, Abhijeet; Travesset, Alex

    2014-03-01

    We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described.

  5. Time-series Photometry of Globular Clusters: M62 (NGC 6266), the Most RR Lyrae-rich Globular Cluster in the Galaxy?

    NASA Astrophysics Data System (ADS)

    Contreras, R.; Catelan, M.; Smith, H. A.; Pritzl, B. J.; Borissova, J.; Kuehn, C. A.

    2010-12-01

    We present new time-series CCD photometry, in the B and V bands, for the moderately metal-rich ([Fe/H] ~= -1.3) Galactic globular cluster M62 (NGC 6266). The present data set is the largest obtained so far for this cluster and consists of 168 images per filter, obtained with the Warsaw 1.3 m telescope at the Las Campanas Observatory and the 1.3 m telescope of the Cerro Tololo Inter-American Observatory, in two separate runs over the time span of 3 months. The procedure adopted to detect the variable stars was the optimal image subtraction method (ISIS v2.2), as implemented by Alard. The photometry was performed using both ISIS and Stetson's DAOPHOT/ALLFRAME package. We have identified 245 variable stars in the cluster fields that have been analyzed so far, of which 179 are new discoveries. Of these variables, 133 are fundamental mode RR Lyrae stars (RRab), 76 are first overtone (RRc) pulsators, 4 are type II Cepheids, 25 are long-period variables (LPVs), 1 is an eclipsing binary, and 6 are not yet well classified. Such a large number of RR Lyrae stars places M62 among the top two most RR Lyrae-rich (in the sense of total number of RR Lyrae stars present) globular clusters known in the Galaxy, second only to M3 (NGC 5272) with a total of 230 known RR Lyrae stars. Since this study covers most but not all of the cluster area, it is not unlikely that M62 is in fact the most RR Lyrae-rich globular cluster in the Galaxy. In like vein, thanks to the time coverage of our data sets, we were also able to detect the largest sample of LPVs known so far in a Galactic globular cluster. We analyze a variety of Oosterhoff type indicators for the cluster, including mean periods, period distribution, Bailey diagrams, and Fourier decomposition parameters (as well as the physical parameters derived therefrom). All of these indicators clearly show that M62 is an Oosterhoff type I system. This is in good agreement with the moderately high metallicity of the cluster, in spite of its

  6. TIME-SERIES PHOTOMETRY OF GLOBULAR CLUSTERS: M62 (NGC 6266), THE MOST RR LYRAE-RICH GLOBULAR CLUSTER IN THE GALAXY?

    SciTech Connect

    Contreras, R.; Catelan, M.; Smith, H. A.; Kuehn, C. A.; Pritzl, B. J.; Borissova, J.

    2010-12-15

    We present new time-series CCD photometry, in the B and V bands, for the moderately metal-rich ([Fe/H] {approx_equal} -1.3) Galactic globular cluster M62 (NGC 6266). The present data set is the largest obtained so far for this cluster and consists of 168 images per filter, obtained with the Warsaw 1.3 m telescope at the Las Campanas Observatory and the 1.3 m telescope of the Cerro Tololo Inter-American Observatory, in two separate runs over the time span of 3 months. The procedure adopted to detect the variable stars was the optimal image subtraction method (ISIS v2.2), as implemented by Alard. The photometry was performed using both ISIS and Stetson's DAOPHOT/ALLFRAME package. We have identified 245 variable stars in the cluster fields that have been analyzed so far, of which 179 are new discoveries. Of these variables, 133 are fundamental mode RR Lyrae stars (RRab), 76 are first overtone (RRc) pulsators, 4 are type II Cepheids, 25 are long-period variables (LPVs), 1 is an eclipsing binary, and 6 are not yet well classified. Such a large number of RR Lyrae stars places M62 among the top two most RR Lyrae-rich (in the sense of total number of RR Lyrae stars present) globular clusters known in the Galaxy, second only to M3 (NGC 5272) with a total of 230 known RR Lyrae stars. Since this study covers most but not all of the cluster area, it is not unlikely that M62 is in fact the most RR Lyrae-rich globular cluster in the Galaxy. In like vein, thanks to the time coverage of our data sets, we were also able to detect the largest sample of LPVs known so far in a Galactic globular cluster. We analyze a variety of Oosterhoff type indicators for the cluster, including mean periods, period distribution, Bailey diagrams, and Fourier decomposition parameters (as well as the physical parameters derived therefrom). All of these indicators clearly show that M62 is an Oosterhoff type I system. This is in good agreement with the moderately high metallicity of the cluster, in spite

  7. Shapiro effect as a possible cause of the low-frequency pulsar timing noise in globular clusters

    NASA Astrophysics Data System (ADS)

    Larchenkova, T. I.; Kopeikin, S. M.

    2006-01-01

    A prolonged timing of millisecond pulsars has revealed low-frequency uncorrelated (infrared) noise, presumably of astrophysical origin, in the pulse arrival time (PAT) residuals for some of them. Currently available pulsar timing methods allow the statistical parameters of this noise to be reliably measured by decomposing the PAT residual function into orthogonal Fourier harmonics. In most cases, pulsars in globular clusters show a low-frequency modulation of their rotational phase and spin rate. The relativistic time delay of the pulsar signal in the curved spacetime of randomly distributed and moving globular cluster stars (the Shapiro effect) is suggested as a possible cause of this modulation. Extremely important (from an astrophysical point of view) information about the structure of the globular cluster core, which is inaccessible to study by other observational methods, could be obtained by analyzing the spectral parameters of the low-frequency noise caused by the Shapiro effect and attributable to the random passages of stars near the line of sight to the pulsar. Given the smallness of the aberration corrections that arise from the nonstationarity of the gravitational field of the randomly distributed ensemble of stars under consideration, a formula is derived for the Shapiro effect for a pulsar in a globular cluster. The derived formula is used to calculate the autocorrelation function of the low-frequency pulsar noise, the slope of its power spectrum, and the behavior of the σz statistic that characterizes the spectral properties of this noise in the form of a time function. The Shapiro effect under discussion is shown to manifest itself for large impact parameters as a low-frequency noise of the pulsar spin rate with a spectral index of n = -1.8 that depends weakly on the specific model distribution of stars in the globular cluster. For small impact parameters, the spectral index of the noise is n = -1.5.

  8. Thrombin mitogenic responses and protein phosphorylation are different in cultured human endothelial cells derived from large and microvessels

    SciTech Connect

    Dupuy, E.; Bikfalvi, A.; Rendu, F.; Toledano, S.L.; Tobelem, G. )

    1989-12-01

    It is well established that thrombin induces various biological responses in endothelial cells derived from large vessels. However, little is known about the effects of thrombin on the microvasculature. Protein phosphorylation may be one of the mechanisms by which an extracellular stimulus initiates cellular events like proliferation. Therefore, we have compared the effects of either human alpha-thrombin or phorbol esters (TPA) on the proliferation or protein phosphorylation in endothelial cells derived from large vessels (umbilical vein, HUVEC) or microvessels (omental tissue, HOMEC). In HOMEC, thrombin did not stimulate cell proliferation and protein phosphorylation while TPA slightly reduced the cell proliferation and induced the phosphorylation of a 27-kDa protein. In contrast, in HUVEC, thrombin or TPA markedly enhanced the cell proliferation and stimulated the phosphorylation of a 59-kDa protein. These data indicate that endothelial cells from large and small vessels respond differently to thrombin and there is a complex and as yet unclear relationship between the proliferation and the protein phosphorylation induced by thrombin.

  9. Efficient large-scale protein production of larvae and pupae of silkworm by Bombyx mori nuclear polyhedrosis virus bacmid system.

    PubMed

    Motohashi, Tomoko; Shimojima, Tsukasa; Fukagawa, Tatsuo; Maenaka, Katsumi; Park, Enoch Y

    2005-01-21

    Silkworm is one of the most attractive hosts for large-scale production of eukaryotic proteins as well as recombinant baculoviruses for gene transfer to mammalian cells. The bacmid system of Autographa californica nuclear polyhedrosis virus (AcNPV) has already been established and widely used. However, the AcNPV does not have a potential to infect silkworm. We developed the first practical Bombyx mori nuclear polyhedrosis virus bacmid system directly applicable for the protein expression of silkworm. By using this system, the green fluorescence protein was successfully expressed in silkworm larvae and pupae not only by infection of its recombinant virus but also by direct injection of its bacmid DNA. This method provides the rapid protein production in silkworm as long as 10 days, is free from biohazard, thus will be a powerful tool for the future production factory of recombinant eukaryotic proteins and baculoviruses. PMID:15596136

  10. A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction.

    PubMed

    Johnson, J; Brackley, C A; Cook, P R; Marenduzzo, D

    2015-02-18

    We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility. PMID:25563801

  11. A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction

    NASA Astrophysics Data System (ADS)

    Johnson, J.; Brackley, C. A.; Cook, P. R.; Marenduzzo, D.

    2015-02-01

    We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.

  12. Are the globular clusters with significant internal [Fe/H] spreads all former dwarf galaxy nuclei?

    NASA Astrophysics Data System (ADS)

    da Costa, G. S.

    2016-08-01

    In this contribution the hypothesis that the Galactic globular clusters with substantial internal [Fe/H] abundance ranges are the former nuclei of disrupted dwarf galaxies is discussed. Evidence considered includes the form of the metallicity distribution function, the occurrence of large diffuse outer envelopes in cluster density profiles, and the presence of ([s-process/Fe], [Fe/H]) correlations. The hypothesis is shown to be plausible but with the caveat that if significantly more than the current nine clusters known to have [Fe/H] spreads are found, then re-evaluation will be required.

  13. Ultraviolet properties of individual hot stars in globular cluster cores. 1: NGC 1904 (M 79)

    NASA Technical Reports Server (NTRS)

    Altner, Bruce; Matilsky, Terry A.

    1992-01-01

    As part of an observing program using the International Ultraviolet Explorer (IUE) satellite to investigate the ultraviolet properties of stars found within the cores of galactic globular clusters with blue horizontal branches (HBs), we obtained three spectra of the cluster NGC 1904 (M 79). All three were long integration-time, short-wavelength (SWP) spectra obtained at the so called 'center of light' and all three showed evidence of sources within the IUE large aperture (21.4 in. by 10 in.). In this paper we shall describe the analysis of these spectra and present evidence that the UV sources represent individual hot stars in the post-HB stage of evolution.

  14. Enrichment by supernovae in globular clusters with multiple populations.

    PubMed

    Lee, Jae-Woo; Kang, Young-Woon; Lee, Jina; Lee, Young-Wook

    2009-11-26

    The most massive globular cluster in the Milky Way, omega Centauri, is thought to be the remaining core of a disrupted dwarf galaxy, as expected within the model of hierarchical merging. It contains several stellar populations having different heavy elemental abundances supplied by supernovae-a process known as metal enrichment. Although M 22 appears to be similar to omega Cen, other peculiar globular clusters do not. Therefore omega Cen and M 22 are viewed as exceptional, and the presence of chemical inhomogeneities in other clusters is seen as 'pollution' from the intermediate-mass asymptotic-giant-branch stars expected in normal globular clusters. Here we report Ca abundances for seven globular clusters and compare them to omega Cen. Calcium and other heavy elements can only be supplied through numerous supernovae explosions of massive stars in these stellar systems, but the gravitational potentials of the present-day clusters cannot preserve most of the ejecta from such explosions. We conclude that these globular clusters, like omega Cen, are most probably the relics of more massive primeval dwarf galaxies that merged and disrupted to form the proto-Galaxy. PMID:19940919

  15. Mitochondrial protein import receptors in Kinetoplastids reveal convergent evolution over large phylogenetic distances

    PubMed Central

    Mani, Jan; Desy, Silvia; Niemann, Moritz; Chanfon, Astrid; Oeljeklaus, Silke; Pusnik, Mascha; Schmidt, Oliver; Gerbeth, Carolin; Meisinger, Chris; Warscheid, Bettina; Schneider, André

    2015-01-01

    Mitochondrial protein import is essential for all eukaryotes and mediated by hetero-oligomeric protein translocases thought to be conserved within all eukaryotes. We have identified and analysed the function and architecture of the non-conventional outer membrane (OM) protein translocase in the early diverging eukaryote Trypanosoma brucei. It consists of six subunits that show no obvious homology to translocase components of other species. Two subunits are import receptors that have a unique topology and unique protein domains and thus evolved independently of the prototype receptors Tom20 and Tom70. Our study suggests that protein import receptors were recruited to the core of the OM translocase after the divergence of the major eukaryotic supergroups. Moreover, it links the evolutionary history of mitochondrial protein import receptors to the origin of the eukaryotic supergroups. PMID:25808593

  16. THE DYNAMICAL EVOLUTION OF STELLAR BLACK HOLES IN GLOBULAR CLUSTERS

    SciTech Connect

    Morscher, Meagan; Pattabiraman, Bharath; Rodriguez, Carl; Rasio, Frederic A.; Umbreit, Stefan

    2015-02-10

    Our current understanding of the stellar initial mass function and massive star evolution suggests that young globular clusters (GCs) may have formed hundreds to thousands of stellar-mass black holes (BHs), the remnants of stars with initial masses from ∼20-100 M {sub ☉}. Birth kicks from supernova explosions may eject some BHs from their birth clusters, but most should be retained. Using a Monte Carlo method we investigate the long-term dynamical evolution of GCs containing large numbers of stellar BHs. We describe numerical results for 42 models, covering a broad range of realistic initial conditions, including up to 1.6 × 10{sup 6} stars. In almost all models we find that significant numbers of BHs (up to ∼10{sup 3}) are retained all the way to the present. This is in contrast to previous theoretical expectations that most BHs should be ejected dynamically within a few gigayears The main reason for this difference is that core collapse driven by BHs (through the Spitzer {sup m}ass segregation instability{sup )} is easily reverted through three-body processes, and involves only a small number of the most massive BHs, while lower-mass BHs remain well-mixed with ordinary stars far from the central cusp. Thus the rapid segregation of stellar BHs does not lead to a long-term physical separation of most BHs into a dynamically decoupled inner core, as often assumed previously. Combined with the recent detections of several BH X-ray binary candidates in Galactic GCs, our results suggest that stellar BHs could still be present in large numbers in many GCs today, and that they may play a significant role in shaping the long-term dynamical evolution and the present-day dynamical structure of many clusters.

  17. INITIAL SIZE DISTRIBUTION OF THE GALACTIC GLOBULAR CLUSTER SYSTEM

    SciTech Connect

    Shin, Jihye; Kim, Sungsoo S.; Yoon, Suk-Jin; Kim, Juhan

    2013-01-10

    Despite the importance of their size evolution in understanding the dynamical evolution of globular clusters (GCs) of the Milky Way, studies that focus specifically on this issue are rare. Based on the advanced, realistic Fokker-Planck (FP) approach, we theoretically predict the initial size distribution (SD) of the Galactic GCs along with their initial mass function and radial distribution. Over one thousand FP calculations in a wide parameter space have pinpointed the best-fit initial conditions for the SD, mass function, and radial distribution. Our best-fit model shows that the initial SD of the Galactic GCs is of larger dispersion than today's SD, and that the typical projected half-light radius of the initial GCs is {approx}4.6 pc, which is 1.8 times larger than that of the present-day GCs ({approx}2.5 pc). Their large size signifies greater susceptibility to the Galactic tides: the total mass of destroyed GCs reaches 3-5 Multiplication-Sign 10{sup 8} M {sub Sun }, several times larger than previous estimates. Our result challenges a recent view that the Milky Way GCs were born compact on the sub-pc scale, and rather implies that (1) the initial GCs were generally larger than the typical size of the present-day GCs, (2) the initially large GCs mostly shrank and/or disrupted as a result of the galactic tides, and (3) the initially small GCs expanded by two-body relaxation, and later shrank by the galactic tides.

  18. [Electron transfer between globular proteins. Evaluation of a matrix element].

    PubMed

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

    1998-01-01

    The dependence of the matrix element of the probability of interprotein electron transfer on the mutual orientation of the donor and acceptor centers and the distance between them was calculated. The calculations were made under the assumption that electron transfer proceeds mainly by a collective excitation of polaron nature, like a solvated electron state. The results obtained are consistent with experimental data and indicate the nonexponential behavior of this dependence in the case when the distance transfer is less than 20 A.

  19. Estimation of Sedimentation Coefficients and Frictional Ratios of Globular Proteins.

    ERIC Educational Resources Information Center

    Smith, Christopher A.

    1988-01-01

    Describes a program to support lectures on analytical centrifugation, and to illustrate the manner in which useful analytical data about macromolecules can be obtained from simple centrifugation studies without the need for mathematical expertise. Discusses the background, methods, calculations, and results involved in this activity. (CW)

  20. Interaction between oppositely charged micelles or globular proteins.

    PubMed

    Wu, J Z; Bratko, D; Blanch, H W; Prausnitz, J M

    2000-10-01

    Monte Carlo simulations and the hypernetted chain theory are used to study the interaction between spherical macroions of opposite charge immersed in a solution of monovalent or divalent simple electrolyte. These calculations represent the first step toward studying phase behavior and precipitation kinetics in solutions containing a mixture of macroions with positive and negative net charges. The potential of mean force between colloidal particles is determined as a function of colloid-colloid separation. In addition to having an opposite sign, the calculated potential of mean force is found to be stronger and longer-ranged than observed in the case of equally charged macroparticles. The difference is more pronounced in the presence of divalent counterions and is especially noticeable when we compare distinct Coulombic and hard-core collision contributions to the interaction between equally and oppositely charged colloids. The present observations suggest the dominance of attractive forces between globally neutral but electrostatically heterogeneous macroparticles. While our numerical results cannot be successfully analyzed by existing theories, they provide useful guidance and benchmark data for the development of advanced analytic descriptions.

  1. Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles.

    PubMed

    Deeb, Sally J; Tyanova, Stefka; Hummel, Michael; Schmidt-Supprian, Marc; Cox, Juergen; Mann, Matthias

    2015-11-01

    Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but this requires accurate and robust tools. Here, we develop a state of the art quantitative mass spectrometric pipeline to characterize formalin-fixed paraffin-embedded tissues of patients with closely related subtypes of diffuse large B-cell lymphoma. We combined a super-SILAC approach with label-free quantification (hybrid LFQ) to address situations where the protein is absent in the super-SILAC standard but present in the patient samples. Shotgun proteomic analysis on a quadrupole Orbitrap quantified almost 9,000 tumor proteins in 20 patients. The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origin using both their global protein expression patterns and the 55-protein signature obtained previously from patient-derived cell lines (Deeb, S. J., D'Souza, R. C., Cox, J., Schmidt-Supprian, M., and Mann, M. (2012) Mol. Cell. Proteomics 11, 77-89). Expression levels of individual segregation-driving proteins as well as categories such as extracellular matrix proteins behaved consistently with known trends between the subtypes. We used machine learning (support vector machines) to extract candidate proteins with the highest segregating power. A panel of four proteins (PALD1, MME, TNFAIP8, and TBC1D4) is predicted to classify patients with low error rates. Highly ranked proteins from the support vector analysis revealed differential expression of core signaling molecules between the subtypes, elucidating aspects of their pathobiology. PMID:26311899

  2. A New Instability Strip in the HR Diagram of Massive Globular Clusters

    NASA Astrophysics Data System (ADS)

    Brown, Thomas

    2012-10-01

    We propose far-UV time-series imaging of the core of NGC 2808, a massive globular cluster exhibiting a triple main sequence, in order to search for pulsators among its large population of hot subdwarfs {a.k.a. extreme horizontal branch stars}. For more than a decade, pulsating subdwarfs were only found in the Galactic field population, where they have enabled precise measurements of stellar parameters through asteroseismology. However, recent observations of the massive globular cluster omega Cen have revealed pulsating subdwarfs clustered at a temperature { 50,000 K} much hotter than those found in the field { 30,000 K}. Globular clusters offer a superior laboratory for studying such pulsators because they avoid the uncertainties in distance, reddening, age, and initial chemical composition that plague the field population. NGC 2808 is the prime target to search for these new pulsators and to characterize their instability strip, given its size, distance, low reddening, and wealth of extant UV data. Our previous UV imaging and spectroscopy of NGC 2808 found a large population of hot subdwarfs with temperatures that span those of both the omega Cen pulsators and the field pulsators. Far-UV time-tag imaging with STIS is the only way that these short-period { 100 sec} pulsators can be found in the NGC 2808 core. The discovery of this new class of pulsators opens the exciting possibility of using asteroseismology to constrain the formation mechanisms of hot subdwarfs {binary mass transfer, mergers, flash mixing, helium-rich subpopulations}, and of exploring the role of iron enhancement via radiative levitation as the driving mechanism for the pulsations.

  3. Mapping the differential reddening in globular clusters

    NASA Astrophysics Data System (ADS)

    Bonatto, C.; Campos, Fabíola; Kepler, S. O.

    2013-10-01

    We build differential-reddening maps for 66 Galactic globular clusters (GCs) with archival Hubble Space Telescope WFC/ACS F606W and F814W photometry. Because of the different GC sizes (characterized by the half-light radius Rh) and distances to the Sun, the WFC/ACS field of view (200 arcsec × 200 arcsec) coverage (Robs) lies in the range 1 ≲ Robs/Rh ≲ 15 for about 85 per cent of the sample, with about 10 per cent covering only the inner (Robs ≲ Rh) parts. We divide the WFC/ACS field of view across each cluster in a regular cell grid and extract the stellar-density Hess diagram from each cell, shifting it in colour and magnitude along the reddening vector until matching the mean diagram. Thus, the maps correspond to the internal dispersion of the reddening around the mean. Depending on the number of available stars (i.e. probable members with adequate photometric errors), the angular resolution of the maps range from ≈ 7 arcsec × 7 arcsec to ≈ 20 arcsec × 20 arcsec. We detect spatially variable extinction in the 66 GCs studied, with mean values ranging from < δE(B-V)> ≡ 0.018 (NGC 6981) up to <δE(B-V)> ≡ 0.016 (Palomar 2). Differential-reddening correction decreases the observed foreground reddening and the apparent distance modulus but, since they are related to the same value of E(B - V), the distance to the Sun is conserved. Fits to the mean-ridge lines of the highly extincted and photometrically scattered GC Palomar 2 show that age and metallicity also remain unchanged after the differential-reddening correction, but measurement uncertainties decrease because of the reduced scatter. The lack of systematic variations of <δE(B-V)> with both the foreground reddening and the sampled cluster area indicates that the main source of differential reddening is interstellar.

  4. Biphasic Synthesis of Large-Pore and Well-Dispersed Benzene Bridged Mesoporous Organosilica Nanoparticles for Intracellular Protein Delivery.

    PubMed

    Yang, Yannan; Niu, Yuting; Zhang, Jun; Meka, Anand Kumar; Zhang, Hongwei; Xu, Chun; Lin, Chun Xiang Cynthia; Yu, Meihua; Yu, Chengzhong

    2015-06-01

    Large pore (4.6-7.6 nm) and well-dispersed benzene bridged mesoporous organosilica nanoparticles with uniform particle size of ≈50 nm are prepared via a biphasic approach. They can be directly used as nanocarriers without surface modification for the intracellular delivery of therapeutic proteins.

  5. Light-element abundance variations in globular clusters

    NASA Astrophysics Data System (ADS)

    Martell, S. L.

    2011-06-01

    Star-to-star variations in abundances of the light elements carbon, nitrogen, oxygen, and sodium have been observed in stars of all evolutionary phases in all Galactic globular clusters that have been thoroughly studied. The data available for studying this phenomenon, and the hypotheses as to its origin, have both co-evolved with observing technology; once high-resolution spectra were available even for main-sequence stars in globular clusters, scenarios involving multiple closely spaced stellar generations enriched by feedback from moderate- and high-mass stars began to gain traction in the literature. This paper briefly reviews the observational history of globular cluster abundance inhomogeneities, discusses the presently favored models of their origin, and considers several aspects of this problem that require further study. Highlight talk Astronomische Gesellschaft 2010

  6. Astronomers Ponder Lack of Planets in Globular Cluster

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This videotape has seven segments, discussing and showing the evidence for the proposition that the galactic clusters do not have many planets. Specifically the segments show: (1) Dr. Ron Gilliland discussing the process of looking for "Hot Jupiters" (i.e., planets about the size of Jupiter, which are hotter than Jupiter) in the globular clusters, (2) a zoom into 47 Tucanae globular cluster, (3) an animation of a planet passing between the host star and the earth with a brightness graph, (4) the same animation as before without the graph, (5) Ron Gilliland of the Space Telescope Science Institute (STScI) discussing possible interpretations of his findings in the 47 Tucanae globular cluster, (6) Ron Gilliland examining the images of 47 Tucanae, and (7) images of 47 Tucanae watching for variations in brightness.

  7. Pulsar-irradiated stars in dense globular clusters

    NASA Technical Reports Server (NTRS)

    Tavani, Marco

    1992-01-01

    We discuss the properties of stars irradiated by millisecond pulsars in 'hard' binaries of dense globular clusters. Irradiation by a relativistic pulsar wind as in the case of the eclipsing millisecond pulsar PSR 1957+20 alter both the magnitude and color of the companion star. Some of the blue stragglers (BSs) recently discovered in dense globular clusters can be irradiated stars in binaries containing powerful millisecond pulsars. The discovery of pulsar-driven orbital modulations of BS brightness and color with periods of a few hours together with evidence for radio and/or gamma-ray emission from BS binaries would valuably contribute to the understanding of the evolution of collapsed stars in globular clusters. Pulsar-driven optical modulation of cluster stars might be the only observable effect of a new class of binary pulsars, i.e., hidden millisecond pulsars enshrouded in the evaporated material lifted off from the irradiated companion star.

  8. The Dynamical Evolution of the Globular Cluster System of M87

    NASA Astrophysics Data System (ADS)

    Kundu, Arunav

    2001-07-01

    We propose to undertake a comprehensive, global analysis of the globular cluster luminosity function {GCLF} of the M87 system using the large amounts of high quality, archival WFPC2 data available in the V {F555W, F606W} and I-bands {F814W}. The data set includes both primary WFPC2 programs with a broad range of science goals, and a large component of deep, parallel data. We propose to accurately determine the parameters of the GCLF, continuously from the core of the galaxy out to a galactocentric radius of 75 Kpc. This will allow us to sensitively test for the radial variation in GCLF properties predicted by various destruction mechanisms. By virtue of the very large database of observations and the richness of the M87 globular cluster system {GCS}, our analysis will provide an observational sample that it at least an order of magnitude more sensitive to radial changes in the GCLF than existing data sets. It will almost certainly become the de facto standard against which current and future evolutionary models of cluster systems are tested. Our proposed study will also allow us to quantify the usefulness of the GCLF as a distance indicator. The accurate determination of the radial profile of the cluster system density function will significantly improve the estimate of the total cluster population, and hence the theoretically important cluster formation efficiency in M87.

  9. A large dataset of protein dynamics in the mammalian heart proteome.

    PubMed

    Lau, Edward; Cao, Quan; Ng, Dominic C M; Bleakley, Brian J; Dincer, T Umut; Bot, Brian M; Wang, Ding; Liem, David A; Lam, Maggie P Y; Ge, Junbo; Ping, Peipei

    2016-03-15

    Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems.

  10. A large dataset of protein dynamics in the mammalian heart proteome

    PubMed Central

    Lau, Edward; Cao, Quan; Ng, Dominic C.M.; Bleakley, Brian J.; Dincer, T. Umut; Bot, Brian M.; Wang, Ding; Liem, David A.; Lam, Maggie P.Y.; Ge, Junbo; Ping, Peipei

    2016-01-01

    Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems. PMID:26977904

  11. Very large G protein-coupled receptor 1 regulates myelin-associated glycoprotein via Gαs/Gαq-mediated protein kinases A/C

    PubMed Central

    Shin, Daesung; Lin, Shu-Ting; Fu, Ying-Hui; Ptáček, Louis J.

    2013-01-01

    VLGR1 (very large G protein-coupled receptor 1), also known as MASS1 (monogenic audiogenic seizure susceptible 1), is an orphan G protein-coupled receptor that contains a large extracellular N terminus with 35 calcium-binding domains. A truncating mutation in the Mass1 gene causes autosomal recessive, sound-induced seizures in the Frings mouse. However, the function of MASS1 and the mechanism underlying Frings mouse epilepsy are not known. Here, we found that MASS1 protein is enriched in the myelinated regions of the superior and inferior colliculi, critical areas for the initiation and propagation of audiogenic seizures. Using a panel of myelin antibodies, we discovered that myelin-associated glycoprotein (MAG) expression is dramatically decreased in Frings mice. MASS1 inhibits the ubiquitylation of MAG, thus enhancing the stability of this protein, and the calcium-binding domains of MASS1 are essential for this regulation. Furthermore, MASS1 interacts with Gαs/Gαq and activates PKA and PKC in response to extracellular calcium. Suppression of signaling by MASS1 RNAi or a specific inhibitor abrogates MAG up-regulation. We postulate that MASS1 senses extracellular calcium and activates cytosolic PKA/PKC pathways to regulate myelination by means of MAG protein stability in myelin-forming cells of the auditory pathway. Further work is required to determine whether MAG dysregulation is a cause or consequence of audiogenic epilepsy and whether there are other pathways regulated by MASS1. PMID:24191038

  12. Integrated UV fluxes and the HB morphology of Globular Clusters

    NASA Astrophysics Data System (ADS)

    Landsman, W. B.; Catelan, M.; O'Connell, R. W.; Pereira, D.; Stecher, T. P.

    2001-12-01

    The UV ( ~ 1500 Å) flux of a globular cluster will be dominated by its blue horizontal branch (HB) population, provided that such a population is present. Thus, the integrated UV - V color of a globular cluster can provide an indication of its HB morphology, without the need to resolve the cluster into a color-magnitude diagram. To date, UV photometry of extragalactic clusters are available for only a few globulars in M31 (e.g. Bohlin et al. 1993, ApJ, 417, 127), but additional UV photometry of extragalactic globulars is soon expected from GALEX (Yi et al. 2001, AAS, 198, 5501), and from STIS FUV-MAMA observations of M87 (HST program 8643). Here we calibrate the relation between UV flux and HB morphology for Galactic globular clusters. The OAO-2 and ANS data tabulated by deBoer (1985, A&A, 142, 321) are supplemented with photometry of 14 globular clusters observed with the Ultraviolet Imaging Telescope (UIT), and a few cluster cores observed with the STIS FUV-MAMA. The UIT data is especially useful since its 40' diameter FOV was sufficient to completely encompass most of the observed clusters, while allowing isolation of hot field and UV-bright stars. We compare the observed Galactic UV color - HB morphology relation with synthetic HB models as a function of age and metallicity. We also estimate the effect of radiative levitation of heavy metals in hot HB stars (e.g. Moehler et al. 2000, , A&A, 360, 120) on the integrated UV flux. This work is funded by STScI grant GO-8358.01.

  13. Cryptosporidium parvum possesses a short-type replication protein A large subunit that differs from its host.

    PubMed

    Zhu, G; Marchewka, M J; Keithly, J S

    1999-07-15

    Replication protein A (RPA) consisting of three subunits is a eukaryotic single-stranded DNA (ssDNA)-binding protein involved in DNA replication, repair and recombination. We report here the identification and characterization of a RPA large subunit (CpRPA1) gene from the apicomplexan Cryptosporidium parvum. The CpRPA1 gene encodes a 53.9-kDa peptide that is remarkably smaller than that from other eukaryotes (i.e. approximately 70 kDa) and is actively expressed in both free sporozoites and parasite intracellular stages. This short-type RPA large subunit has also been characterized from one other protist, Crithidia fasciculata. Three distinct domains have been identified in the RPA large subunit of humans and yeasts: an N-terminal protein interaction domain, a central ssDNA-binding area, and a C-terminal subunit-interacting region. Sequence analysis reveals that the short-type RPA large subunit differs from that of other eukaryotes in that only the domains required for ssDNA binding and heterotrimer formation are present. It lacks the N-terminal domain necessary for the binding of proteins mainly involved in DNA repair and recombination. This major structural difference suggests that the mechanism for DNA repair and recombination in some protists differs from that of other eukaryotes. Since replication proteins play an essential role in the cell cycle, the fact that RPA proteins of C. parvum differ from those of its host suggests that RPA be explored as a potential chemotherapeutic target for controlling cryptosporidiosis and/or diseases caused by other apicomplexans.

  14. Maize (Zea mays)-derived bovine trypsin: characterization of the first large-scale, commercial protein product from transgenic plants.

    PubMed

    Woodard, Susan L; Mayor, Jocelyne M; Bailey, Michele R; Barker, Donna K; Love, Robert T; Lane, Jeffrey R; Delaney, Donna E; McComas-Wagner, Janet M; Mallubhotla, Hanuman D; Hood, Elizabeth E; Dangott, Lawrence J; Tichy, Shane E; Howard, John A

    2003-10-01

    Bovine trypsin (EC 3.4.21.4) is an enzyme that is widely used for commercial purposes to digest or process other proteins, including some therapeutic proteins. The biopharmaceutical industry is trying to eliminate animal-derived proteins from manufacturing processes due to the possible contamination of these products by human pathogens. Recombinant trypsin has been produced in a number of systems, including cell culture, bacteria and yeast. To date, these expression systems have not produced trypsin on a scale sufficient to fulfill the need of biopharmaceutical manufacturers where kilogram quantities are often required. The present paper describes commercial-level production of trypsin in transgenic maize (Zea mays) and its physical and functional characterization. This protease, the first enzyme to be produced on a large-scale using transgenic plant technology, is functionally equivalent to native bovine pancreatic trypsin. The availability of this reagent should allow for the replacement of animal-derived trypsin in the processing of pharmaceutical proteins.

  15. Robotic large-scale application of wheat cell-free translation to structural studies including membrane proteins.

    PubMed

    Beebe, Emily T; Makino, Shin-Ichi; Nozawa, Akira; Matsubara, Yuko; Frederick, Ronnie O; Primm, John G; Goren, Michael A; Fox, Brian G

    2011-04-30

    The use of the Protemist XE, an automated discontinuous-batch protein synthesis robot, in cell-free translation is reported. The soluble Galdieria sulphuraria protein DCN1 was obtained in greater than 2mg total synthesis yield per mL of reaction mixture from the Protemist XE, and the structure was subsequently solved by X-ray crystallography using material from one 10 mL synthesis (PDB ID: 3KEV). The Protemist XE was also capable of membrane protein translation. Thus human sigma-1 receptor was translated in the presence of unilamellar liposomes and bacteriorhodopsin was translated directly into detergent micelles in the presence of all-trans-retinal. The versatility, ease of use, and compact size of the Protemist XE robot demonstrate its suitability for large-scale synthesis of many classes of proteins.

  16. Photometry of Multiple Stellar Populations in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Milone, Antonino

    2012-05-01

    An increasing number of observations over the last years have shown the existence of distinct sub-populations in many (maybe all) globular clusters and shattered the paradigm of globulars hosting single, simple stellar populations. These multiple populations manifest themselves in a split of different evolutionary sequences in the cluster color-magnitude diagrams. Using filters covering an appropriate range of wavelengths, photometry splits the main sequence into two or more branches, and in many cases this bimodality is repeated in the subgiant and red giant regions, and on the horizontal branch. In this talk I will summarize the main results from photometric studies.

  17. Sistemas de cúmulos globulares extragalácticos

    NASA Astrophysics Data System (ADS)

    Forte, J. C.

    Se describen las características de los sistemas de cúmulos globulares asociados a galaxias elípticas en una variedad de medios y, en particular, aquellas vinculadas con la distribución espacial, frecuencia específica y composición química. Esta discusión se hace dentro de un conjunto de esquemas orientados a explicar las primeras fases de la formación de las galaxias dominantes en cúmulos y del rol de los sistemas de cúmulos globulares en esos procesos.

  18. A Guided Tour of Globular Clusters in the Local Group

    NASA Astrophysics Data System (ADS)

    Sarajedini, Ata

    2010-05-01

    I will lead a guided tour of the globular cluster systems of Local Group galaxies. Beginning with the Milky Way, I will attempt to compare and contrast the properties of the globular clusters in the Sagittarius and Fornax dwarf spheroidals, the LMC, M31, and M33. Along the way, I will concentrate on why these clusters are important and how our understanding of their properties has changed over time. Because of the limited time available, this tour will necessarily be incomplete, but I hope to give the audience a flavor for how active and vibrant this field continues to be.

  19. Simulations of Globular Clusters Merging in Galactic Nuclear Regions

    NASA Astrophysics Data System (ADS)

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

    We present the results of detailed N-body simulations regarding the interaction of four massive globular clusters in the central region of a triaxial galaxy. The systems undergo a full merging event, producing a sort of `Super Star Cluster' (SSC) whose features are close to those of a superposition of the individual initial mergers. In contrast with other similar simulations, the resulting SSC structural parameters are located along the observed scaling relations of globular clusters. These findings seem to support the idea that a massive SSC may have formed in early phases of the mother galaxy evolution and contributed to the growth of a massive nucleus.

  20. Proteomic Analysis of Pure Human Airway Gland Mucus Reveals a Large Component of Protective Proteins

    PubMed Central

    Joo, Nam Soo; Evans, Idil Apak T.; Cho, Hyung-Ju; Park, Il-Ho; Engelhardt, John F.; Wine, Jeffrey J.

    2015-01-01

    Airway submucosal glands contribute to innate immunity and protect the lungs by secreting mucus, which is required for mucociliary clearance and which also contains antimicrobial, anti-inflammatory, anti-proteolytic and anti-oxidant proteins. We stimulated glands in tracheal trimmings from three lung donors and collected droplets of uncontaminated mucus as they formed at the gland orifices under an oil layer. We analyzed the mucus using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Analysis identified 5486 peptides and 441 proteins from across the 3 samples (269–319 proteins per subject). We focused on 269 proteins common to at least 2 0f 3 subjects, of which 102 (38%) had protective or innate immunity functions. While many of these have long been known to play such roles, for many others their cellular protective functions have only recently been appreciated in addition to their well-studied biologic functions (e.g. annexins, apolipoproteins, gelsolin, hemoglobin, histones, keratins, and lumican). A minority of the identified proteins are known to be secreted via conventional exocytosis, suggesting that glandular secretion occurs via multiple mechanisms. Two of the observed protective proteins, major vault protein and prohibitin, have not been observed in fluid from human epithelial cultures or in fluid from nasal or bronchoalveolar lavage. Further proteomic analysis of pure gland mucus may help clarify how healthy airways maintain a sterile environment. PMID:25706550

  1. Exploring Symmetry as an Avenue to the Computational Design of Large Protein Domains

    SciTech Connect

    Fortenberry, Carie; Bowman, Elizabeth Anne; Proffitt, Will; Dorr, Brent; Combs, Steven; Harp, Joel; Mizoue, Laura; Meiler, Jens

    2012-03-15

    It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements - 'symmetric superfolds'. Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric ({beta}{alpha}){sub 8} TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.

  2. Controlled Charge Trapping and Retention in Large-Area Monodisperse Protein Metal-Nanoparticle Conjugates.

    PubMed

    Kim, Chang-Hyun; Bhak, Ghibom; Lee, Junghee; Sung, Sujin; Park, Sungjun; Paik, Seung R; Yoon, Myung-Han

    2016-05-18

    Here, we report on charge-retention transistors based on novel protein-mediated Au nanoparticle (NP) arrays, with precise control over dimension and distribution. Individual NPs are coated with alpha-synuclein, an amyloidogenic protein responsible for Lewy body formation in Parkinson's disease. Subsequently, a monolayer of protein-NP conjugates is successfully created via a simple and scalable solution deposition to function as distributed nanoscale capacitors. Controllability over the film structure translates into the tunability of the electrical performance; pentacene-based organic transistors feature widely varying programmability and relaxation dynamics, providing versatility for various unconventional memory applications. PMID:27144458

  3. Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis

    PubMed Central

    Riley, Robert; Pellegrini, Matteo; Eisenberg, David

    2008-01-01

    We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs. To illustrate the problem, we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis. Our computational method uses structural information, operon organization, and protein coevolution to infer the interaction of PE and PPE proteins. Some 289 PE/PPE complexes were predicted out of a possible 5,590 PE/PPE pairs genomewide. Thirty-five of these predicted complexes were also found to have correlated mRNA expression, providing additional evidence for these interactions. We show that our method is applicable to other protein families, by analyzing interactions of the Esx family of proteins. Our resulting set of predictions is a starting point for genomewide experimental interaction screens of the PE and PPE families, and our method may be generally useful for detecting interactions of proteins within families having many paralogs. PMID:18787688

  4. Fukuyoa paulensis gen. et sp. nov., a New Genus for the Globular Species of the Dinoflagellate Gambierdiscus (Dinophyceae)

    PubMed Central

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M.; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi / G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov. PMID:25831082

  5. Fukuyoa paulensis gen. et sp. nov., a new genus for the globular species of the dinoflagellate Gambierdiscus (Dinophyceae).

    PubMed

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi/G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov.

  6. The Evolution of the Globular Cluster System in a Triaxial Galaxy: Can a Galactic Nucleus Form by Globular Cluster Capture?

    NASA Astrophysics Data System (ADS)

    Capuzzo-Dolcetta, Roberto

    1993-10-01

    Among the possible phenomena inducing evolution of the globular cluster system in an elliptical galaxy, dynamical friction due to field stars and tidal disruption caused by a central nucleus is of crucial importance. The aim of this paper is the study of the evolution of the globular cluster system in a triaxial galaxy in the presence of these phenomena. In particular, the possibility is examined that some galactic nuclei have been formed by frictionally decayed globular clusters moving in a triaxial potential. We find that the initial rapid growth of the nucleus, due mainly to massive clusters on box orbits falling in a short time scale into the galactic center, is later slowed by tidal disruption induced by the nucleus itself on less massive clusters in the way described by Ostriker, Binney, and Saha. The efficiency of dynamical friction is such to carry to the center of the galaxy enough globular cluster mass available to form a compact nucleus, but the actual modes and results of cluster-cluster encounters in the central potential well are complicated phenomena which remains to be investigated. The mass of the resulting nucleus is determined by the mutual feedback of the described processes, together with the initial spatial, velocity, and mass distributions of the globular cluster family. The effect on the system mass function is studied, showing the development of a low- and high-mass turnover even with an initially flat mass function. Moreover, in this paper is discussed the possibility that the globular cluster fall to the galactic center has been a cause of primordial violent galactic activity. An application of the model to M31 is presented.

  7. The Emerging Role of Large Immunophilin FK506 Binding Protein 51 in Cancer

    PubMed Central

    Romano, S; Sorrentino, A; Di Pace, AL; Nappo, G; Mercogliano, C; Romano, MF

    2011-01-01

    FK506 binding protein 51 (FKBP51) is an immunophilin physiologically expressed in lymphocytes. Very recently, aberrant expression of this protein was found in melanoma; FKBP51 expression correlates with melanoma aggressiveness and is maximal in metastatic lesions. FKBP51 promotes NF-κB activation and is involved in the resistance to genotoxic agents, including anthracyclines and ionizing radiation. FKBP51 is a cochaperone with peptidyl-prolyl isomerase activity that regulates several biological processes through protein-protein interaction. There is increasing evidence that FKBP51 hyperexpression is associated with cancer and this protein has a relevant role in sustaining cell growth, malignancy, and resistance to therapy. There is also evidence that FKBP ligands are potent anticancer agents, in addition to their immunosuppressant activity. In particular, rapamycin and its analogs have shown antitumor activity across a variety of human cancers in clinical trials. Although, classically, rapamycin actions are ascribed to inhibition of mTOR, recent studies indicate FKBP51 is also an important molecular determinant of the drug’s anticancer activity. The aim of this article is to review the functions of FKBP51, especially in view of the recent findings that this protein is a potential oncogene when deregulated and a candidate target for signaling therapies against cancer. PMID:22087835

  8. Distribution of Lick Indices in the Globular Cluster NGC 2808

    NASA Astrophysics Data System (ADS)

    O'Connell, Julia

    2012-01-01

    We have analyzed low resolution spectra for a large sample ( 200) of red giant branch (RGB) stars in the Galactic globular cluster NGC 2808 for indications of bimodality with respect to Lick indices and radial dispersion. Target stars were observed in nine fields over 5 nights in March 2010 with the Blanco 4m telescope and Hydra multi--object positioner and bench spectrograph located at Cerro Tololo Inter--American Observatory. The full wavelength coverage spans from 3900--8200 A; for nights 1 and 2, and from 4500--6950 A; for nights 3, 4, and 5. The low resolution data ( 500 for nights 1 and 2, 1200 for nights 3, 4, and 5; 70) were used to measure radial velocities (RVs) and to determine cluster membership. RVs were measured with the IRAF task xcsao using stars with known radial RVs included in our observed fields as templates. Template candidates were taken from Cacciari et al. (2004) and Carretta et al. (2006), and cross--matched by RA and Dec to stars in our sample. A conservative approach was adopted when including stars as cluster members, with RV= 101.9 ± 7.17 km s-1 (σ=2.83). Indexf was employed to measure 12 Lick indices, with particular attention to CN1, CN2 and Na. The peak distribution of these indices appears to be correlated in stars 2.5--3.5 arc minutes from the cluster center. The correlation becomes less apparent in stars outside this radius.

  9. STELLAR COLLISIONS AND BLUE STRAGGLER STARS IN DENSE GLOBULAR CLUSTERS

    SciTech Connect

    Chatterjee, Sourav; Rasio, Frederic A.; Sills, Alison; Glebbeek, Evert

    2013-11-10

    Blue straggler stars (BSSs) are abundantly observed in all Galactic globular clusters (GGCs) where data exist. However, observations alone cannot reveal the relative importance of various formation channels or the typical formation times for this well-studied population of anomalous stars. Using a state-of-the-art Hénon-type Monte Carlo code that includes all relevant physical processes, we create 128 models with properties typical of the observed GGCs. These models include realistic numbers of single and binary stars, use observationally motivated initial conditions, and span large ranges in central density, concentration, binary fraction, and mass. Their properties can be directly compared with those of observed GGCs. We can easily identify the BSSs in our models and determine their formation channels and birth times. We find that for central densities above ∼10{sup 3} M{sub ☉} pc{sup –3}, the dominant formation channel is stellar collisions, while for lower density clusters, mass transfer in binaries provides a significant contribution (up to 60% in our models). The majority of these collisions are binary-mediated, occurring during three-body and four-body interactions. As a result, a strong correlation between the specific frequency of BSSs and the binary fraction in a cluster can be seen in our models. We find that the number of BSSs in the core shows only a weak correlation with the collision rate estimator Γ traditionally used by observers, in agreement with the latest Hubble Space Telescope Advanced Camera for Surveys data. Using an idealized 'full mixing' prescription for collision products, our models indicate that the BSSs observed today may have formed several Gyr ago. However, denser clusters tend to have younger (∼1 Gyr) BSSs.

  10. Terzan 8: a Sagittarius-flavoured globular cluster

    NASA Astrophysics Data System (ADS)

    Carretta, E.; Bragaglia, A.; Gratton, R. G.; D'Orazi, V.; Lucatello, S.; Sollima, A.

    2014-01-01

    Massive globular clusters (GCs) contain at least two generations of stars with slightly different ages and clearly distinct light element abundances. The Na-O anticorrelation is the best studied chemical signature of multiple stellar generations. Instead, low-mass clusters usually appear to be chemically homogeneous. We are investigating low-mass GCs to understand what the lower mass limit is where multiple populations can form, mainly using the Na and O abundance distribution. We used VLT/FLAMES spectra of giants in the low-mass, metal-poor GC Terzan 8 that belongs to the Sagittarius dwarf galaxy to determine abundances of Fe, O, Na, α-, Fe-peak, and neutron-capture elements in six stars observed with UVES and 14 observed with GIRAFFE. The average metallicity is [Fe/H] = -2.27 ± 0.03 (rms = 0.08), based on the six high-resolution UVES spectra. Only one star, observed with GIRAFFE, shows an enhanced abundance of Na and we tentatively assign it to the second generation. In this cluster, unlike what happens in more massive GCs, the second generation seems to represent at most a minority fraction. We discuss the implications of our findings, comparing Terzan 8 with the other Sgr dSph GCs, and to GCs and field stars in the Large Magellanic Cloud, Fornax, and in other dwarfs galaxies. Based on observations collected at ESO telescopes under programme 087.B-0086Tables 2, 3, 7-10 are available in electronic form at http://www.aanda.orgFull Table 2 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/561/A87

  11. Photometric and kinematic studies of extragalactic globular cluster systems

    NASA Astrophysics Data System (ADS)

    Dowell, Jessica

    Globular clusters (GCs) are old, luminous, compact collections of stars found in galaxy halos that formed during the early stages of galaxy formation. Because of this, GCs serve as excellent tracers of the formation, structure, and merger history of their host galaxies. My dissertation will examine both the photometric and kinematic properties of GC systems and their relationship to their host galaxies. In the first section, I will present the analysis of the GC systems of two spiral galaxies, NGC 891 and NGC 1055. I will discuss the photometric methods used to detect GCs using wide-field BVR imaging and to quantify the global properties of the system such as the total number of GCs and their radial distribution. My results for these two GC systems were compared to those of other galaxies. I will also present the results of spectroscopic follow-up for two giant galaxies: the S0 galaxy NGC 4594 (M104), and the elliptical galaxy NGC 3379 (M105). I measured the radial velocities of GCs in these two galaxies, and combined them with published results to determine the mass distribution and mass-to-light (M/L) ratio profile for each galaxy out to large effective radius (7-9 Re). For both galaxies, I found that the M/L profiles increase with radius and do not flatten, which suggests that the dark matter halos in these galaxies extend to the edge of my data. I also looked for evidence of rotation in the GC systems, and found that neither system exhibits significant rotation around the host galaxy. I examined the velocity dispersion profile of each GC system and found kinematic differences between the red and blue GC subpopulations. Finally, I compared my results to mass estimates for these galaxies from other kinematic tracers and considered them in the context of galaxy formation models.

  12. The Globular Cluster System of the Spiral Galaxy NGC 7814

    NASA Astrophysics Data System (ADS)

    Rhode, Katherine L.; Zepf, Stephen E.

    2003-11-01

    We present the results of a wide-field photometric study of the globular cluster (GC) system of the edge-on Sab spiral NGC 7814. This is the first spiral to be fully analyzed from our survey of the GC systems of a large sample of galaxies beyond the Local Group. NGC 7814 is of particular interest because a previous study estimated that it has 500-1000 GCs, giving it the largest specific frequency (SN) known for a spiral. Understanding this galaxy's GC system is important in terms of our understanding of the GC populations of spirals in general and has implications for the formation of massive galaxies. We observed the galaxy in BVR filters with the WIYN 3.5 m telescope and used image classification and three-color photometry to select GC candidates. We also analyzed archival Hubble Space Telescope (HST) Wide Field Planetary Camera 2 images of NGC 7814, both to help quantify the contamination level of the WIYN GC candidate list and to detect GCs in the inner part of the galaxy halo. Combining HST data with high-quality ground-based images allows us to trace the entire radial extent of this galaxy's GC system and determine the total number of GCs directly through observation. We find that rather than being an especially high-SN spiral, NGC 7814 has <~200 GCs and SN~1, making it comparable to the two most well-studied spiral galaxies, the Milky Way and M31. We explore the implications of these results for models of the formation of galaxies and their GC systems. The initial results from our survey suggest that the GC systems of typical elliptical galaxies can be accounted for by the merger of two or more spirals, but that for highly luminous elliptical galaxies, additional physical processes may be needed.

  13. Hepatitis B virus large surface protein is not secreted but is immunogenic when selectively expressed by recombinant vaccinia virus.

    PubMed Central

    Cheng, K C; Smith, G L; Moss, B

    1986-01-01

    The envelope region of the hepatitis B virus (HBV) genome contains an open reading frame that begins upstream of the major surface protein gene. The two minor proteins that are initiated within this pre-s segment are immunogenic and may be involved in virus attachment to hepatocytes. We have constructed a recombinant vaccinia virus that contains the predicted coding segment for the large surface protein (LS) under control of a vaccinia virus that contains the predicted coding segment for the large surface protein (LS) under control of a vaccinia virus promoter. Cells infected with the recombinant virus synthesized HBV polypeptides of 39 and 42 kilodaltons, corresponding to the unglycosylated and glycosylated forms of LS, respectively. The presence of pre-s epitopes in the 39- and 42-kilodalton polypeptides was demonstrated by binding of antibody prepared against a synthetic peptide. Synthesis of the 42-kilodalton species was specifically inhibited by tunicamycin, suggesting that it is N-glycosylated. Despite apparent glycosylation, LS was not secreted into the medium of infected cells. Nevertheless, rabbits vaccinated with the purified recombinant virus made antibodies that recognized s and pre-s epitopes. Antibody to the NH2 terminus of LS appeared before or simultaneously with antibody that bound to the major surface protein. The additional immunogenicity provided by expression of LS may be advantageous for the development of an HBV vaccine. Images PMID:2430108

  14. The Bacterial Intimins and Invasins: A Large and Novel Family of Secreted Proteins

    PubMed Central

    Tsai, Jennifer C.; Yen, Ming-Ren; Castillo, Rostislav; Leyton, Denisse L.; Henderson, Ian R.; Saier, Milton H.

    2010-01-01

    Background Gram-negative bacteria have developed a limited repertoire of solutions for secreting proteins from the cytoplasmic compartment to the exterior of the cell. Amongst the spectrum of secreted proteins are the intimins and invasins (the Int/Inv family; TC# 1.B.54) which are characterized by an N-terminal β-barrel domain and a C-terminal surface localized passenger domain. Despite the important role played by members of this family in diseases mediated by several species of the Enterobacteriaceae, there has been little appreciation for the distribution and diversity of these proteins amongst Gram-negative bacteria. Furthermore, there is little understanding of the molecular events governing secretion of these proteins to the extracellular milieu. Principal Findings In silico approaches were used to analyze the domain organization and diversity of members of this secretion family. Proteins belonging to this family are predominantly associated with organisms from the γ-proteobacteria. Whilst proteins from the Chlamydia, γ-, β- and ε-proteobacteria possess β-barrel domains and passenger domains of various sizes, Int/Inv proteins from the α-proteobacteria, cyanobacteria and chlorobi possess only the predicted β-barrel domains. Phylogenetic analyses revealed that with few exceptions these proteins cluster according to organismal type, indicating that divergence occurred contemporaneously with speciation, and that horizontal transfer was limited. Clustering patterns of the β-barrel domains correlate well with those of the full-length proteins although the passenger domains do so with much less consistency. The modular subdomain design of the passenger domains suggests that subdomain duplication and deletion have occurred with high frequency over evolutionary time. However, all repeated subdomains are found in tandem, suggesting that subdomain shuffling occurred rarely if at all. Topological predictions for the β-barrel domains are presented. Conclusion

  15. Highly efficient immunodiagnosis of Large cardamom chirke virus using the polyclonal antiserum against Escherichia coli expressed recombinant coat protein.

    PubMed

    Vijayanandraj, S; Yogita, M; Das, Amrita; Ghosh, Amalendu; Mandal, Bikash

    2013-09-01

    Large cardamom chirke virus (LCCV), genus Macluravirus, family Potyviridae is an important constrain in large cardamom production in India. Purification of LCCV from large cardamom tissues is difficult and therefore immunodiagnostic reagents are not available. In the present study, we have successfully expressed coat protein (CP) gene of LCCV in Escherichia coli. The purification of expressed protein by Ni-NTA affinity chromatography was inefficient due to precipitation of protein during renaturation. We have optimized a simple, inexpensive and efficient method for purification of the expressed CP through gel extraction with 5 % SDS followed by renaturation in Milli-Q water, which resulted in high yield (4.7 mg/ml) and good quality of the protein. A higher titer (1:256,000) polyclonal antibody (PAb) to the recombinant CP was produced, which strongly recognized LCCV in crude leaf extract and showed minimal background reaction with the healthy leaf extract in enzyme linked immunosorbent assay (ELISA) and dot immunobinding assay (DIBA). The sensitivities of the ELISA and DIBA were 5 and 0.1 ng of expressed protein, respectively. Both the ELISA and DIBA were validated with 100 % accuracy in detecting LCCV in field samples. The PAb differentiated Cardamom mosaic virus, another close relative of LCCV. Our study is first to report highly efficient immunodiagnosis with PAb to E. coli expressed recombinant CP of a virus under the genus Macluravirus. The antigen expression construct and PAb developed in the present study will be useful in production of virus free planting materials of large cardamom. PMID:24426280

  16. Highly efficient immunodiagnosis of Large cardamom chirke virus using the polyclonal antiserum against Escherichia coli expressed recombinant coat protein.

    PubMed

    Vijayanandraj, S; Yogita, M; Das, Amrita; Ghosh, Amalendu; Mandal, Bikash

    2013-09-01

    Large cardamom chirke virus (LCCV), genus Macluravirus, family Potyviridae is an important constrain in large cardamom production in India. Purification of LCCV from large cardamom tissues is difficult and therefore immunodiagnostic reagents are not available. In the present study, we have successfully expressed coat protein (CP) gene of LCCV in Escherichia coli. The purification of expressed protein by Ni-NTA affinity chromatography was inefficient due to precipitation of protein during renaturation. We have optimized a simple, inexpensive and efficient method for purification of the expressed CP through gel extraction with 5 % SDS followed by renaturation in Milli-Q water, which resulted in high yield (4.7 mg/ml) and good quality of the protein. A higher titer (1:256,000) polyclonal antibody (PAb) to the recombinant CP was produced, which strongly recognized LCCV in crude leaf extract and showed minimal background reaction with the healthy leaf extract in enzyme linked immunosorbent assay (ELISA) and dot immunobinding assay (DIBA). The sensitivities of the ELISA and DIBA were 5 and 0.1 ng of expressed protein, respectively. Both the ELISA and DIBA were validated with 100 % accuracy in detecting LCCV in field samples. The PAb differentiated Cardamom mosaic virus, another close relative of LCCV. Our study is first to report highly efficient immunodiagnosis with PAb to E. coli expressed recombinant CP of a virus under the genus Macluravirus. The antigen expression construct and PAb developed in the present study will be useful in production of virus free planting materials of large cardamom.

  17. Purification and Structural Analysis of LEM-Domain Proteins.

    PubMed

    Herrada, Isaline; Bourgeois, Benjamin; Samson, Camille; Buendia, Brigitte; Worman, Howard J; Zinn-Justin, Sophie

    2016-01-01

    LAP2-emerin-MAN1 (LEM)-domain proteins are modular proteins characterized by the presence of a conserved motif of about 50 residues. Most LEM-domain proteins localize at the inner nuclear membrane, but some are also found in the endoplasmic reticulum or nuclear interior. Their architecture has been analyzed by predicting the limits of their globular domains, determining the 3D structure of these domains and in a few cases calculating the 3D structure of specific domains bound to biological targets. The LEM domain adopts an α-helical fold also found in SAP and HeH domains of prokaryotes and unicellular eukaryotes. The LEM domain binds to BAF (barrier-to-autointegration factor; BANF1), which interacts with DNA and tethers chromatin to the nuclear envelope. LAP2 isoforms also share an N-terminal LEM-like domain, which binds DNA. The structure and function of other globular domains that distinguish LEM-domain proteins from each other have been characterized, including the C-terminal dimerization domain of LAP2α and C-terminal WH and UHM domains of MAN1. LEM-domain proteins also have large intrinsically disordered regions that are involved in intra- and intermolecular interactions and are highly regulated by posttranslational modifications in vivo.

  18. Evidence for an inhibitory feedback loop regulating simian virus 40 large T-antigen fusion protein nuclear transport.

    PubMed Central

    Seydel, U; Jans, D A

    1996-01-01

    Nuclear protein import is central to eukaryotic cell function. It is dependent on ATP, temperature and cytosolic factors, and requires specific targeting sequences called nuclear localization signals (NLSs). Nuclear import kinetics was studied in vitro using digitonin-permeabilized cells of the HTC rat hepatoma cell line and a fluorescently labelled beta-galactosidase fusion protein carrying amino acids 111-135 of the simian virus 40 large T-antigen (T-ag), including the NLS. Nuclear accumulation was rapid, reaching steady-state after about 80 min at 37 degrees C (t1/2 at about 17 min). Surprisingly, maximal nuclear concentration was found to be directly proportional to the concentration of the cytosolic extract and of cytoplasmic T-ag protein. Neither preincubation of cells for 1 h at 37 degrees C before the addition of T-ag protein nor the addition of fresh transport medium after 1 h and continuation of the incubation for another hour affected the maximal nuclear concentration. If cells were allowed to accumulate T-ag protein for 1 h before the addition of fresh transport medium containing different concentrations of T-ag protein and incubated for a further hour, the maximal nuclear concentration did not change unless the concentration of T-ag protein in the second transport mixture exceeded that in the first, in which case the nuclear concentration increased. Nuclear import of T-ag thus appeared (i) to be strictly unidirectional over 2 h at 37 degrees C and (ii) to be regulated by an inhibitory feedback loop, whereby the cytosolic concentration of protein appears to determine directly the precise end point of nuclear accumulation. This study represents the first characterization of this previously undescribed mechanism of regulation of nuclear protein import. PMID:8670127

  19. Oncogenic activation of the human trk proto-oncogene by recombination with the ribosomal large subunit protein L7a.

    PubMed Central

    Ziemiecki, A; Müller, R G; Fu, X C; Hynes, N E; Kozma, S

    1990-01-01

    The trk-2h oncogene, isolated from the human breast carcinoma cell line MDA-MB 231 by genomic DNA-transfection into NIH3T3 cells, consists of the trk proto-oncogene receptor kinase domain fused to a N-terminal 41 amino acid activating sequence (Kozma, S.C., Redmond, S.M.S., Xiao-Chang, F., Saurer, S.M., Groner, B. and Hynes, N.E. (1988) EMBO J., 7, 147-154). Antibodies raised against a bacterially produced beta gal-trk receptor kinase fusion protein recognized a 44 kd phosphoprotein phosphorylated on serine, threonine and tyrosine in extracts of trk-2h transformed NIH3T3 cells. In vitro, in the presence of Mn2+/gamma ATP, this protein became phosphorylated extensively on tyrosine. Cells transformed by trk-2h did not, however, show an elevation in total phosphotyrosine. We have cloned and sequenced the cDNA encoding the amino terminal activating sequences of trk-2h (Kozma et al., 1988). The encoded protein has a high basic amino acid content and the gene is expressed as an abundant 1.2 kb mRNA in human, rat and mouse cells. Antipeptide antibodies raised against a C-terminal peptide recognized specifically a 30 kd protein on Western blots of human, rat and mouse cell extracts. Immunofluorescence revealed, in addition to granular cytoplasmic fluorescence, intense nucleolar staining. The high basic amino acid content and nucleolar staining prompted us to investigate whether the 30 kd protein could be a ribosomal protein. Western immunoblotting analysis of 2D-electrophoretically resolved ribosomal proteins indicated that the 30 kd protein is the ribosomal large subunit protein L7a.(ABSTRACT TRUNCATED AT 250 WORDS) Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 9. PMID:2403926

  20. Heavy elements in globular clusters: The role of asymptotic giant branch stars

    SciTech Connect

    Straniero, O.; Cristallo, S.; Piersanti, L.

    2014-04-10

    Recent observations of heavy elements in globular clusters reveal intriguing deviations from the standard paradigm of the early galactic nucleosynthesis. If the r-process contamination is a common feature of halo stars, s-process enhancements are found in a few globular clusters only. We show that the combined pollution of asymptotic giant branch (AGB) stars with a mass ranging between 3 to 6 M {sub ☉} may account for most of the features of the s-process overabundance in M4 and M22. In these stars, the s process is a mixture of two very different neutron-capture nucleosynthesis episodes. The first is due to the {sup 13}C(α, n){sup 16}O reaction and takes place during the interpulse periods. The second is due to the {sup 22}Ne(α, n){sup 25}Mg reaction and takes place in the convective zones generated by thermal pulses. The production of the heaviest s elements (from Ba to Pb) requires the first neutron burst, while the second produces large overabundances of light s (Rb, Sr, Y, Zr). The first mainly operates in the less massive AGB stars, while the second dominates in the more massive. From the heavy-s/light-s ratio, we derive that the pollution phase should last for 150 ± 50 Myr, a period short enough compared to the formation timescale of the globular cluster system, but long enough to explain why the s-process pollution is observed in a few cases only. With few exceptions, our theoretical prediction provides a reasonable reproduction of the observed s-process abundances, from Sr to Hf. However, Ce is probably underproduced by our models, while Rb and Pb are overproduced. Possible solutions are discussed.

  1. GeMS MCAO observations of the Galactic globular cluster NGC 2808: the absolute age

    NASA Astrophysics Data System (ADS)

    Massari, D.; Fiorentino, G.; McConnachie, A.; Bono, G.; Dall'Ora, M.; Ferraro, I.; Iannicola, G.; Stetson, P. B.; Turri, P.; Tolstoy, E.

    2016-02-01

    Context. Globular clusters are the oldest stellar systems in the Milky Way, and they probe the early epoch of the Galaxy formation. However, the uncertainties on their absolute age are still too large to soundly constrain how the Galactic structures have assembled. Aims: The aim of this work is to obtain an accurate estimate of the absolute age of the globular cluster NGC 2808 using deep IR data obtained with the multi-conjugate adaptive optics system operating at the Gemini South telescope (GeMS). Methods: This exquisite photometry, combined with that obtained in V and I-bands with HST, allowed us to detect the faint Main Sequence Knee feature in NGC 2808 colour magnitude diagram. The difference between this point and the main sequence turn-off is a good age estimator that provides ages with unprecedented accuracy. Results: We find that NGC 2808 has an age of t = 10.9 ± 0.7 (intrinsic) ±0.45 (metallicity term) Gyr. A possible contamination by He-enhanced population could make the cluster up to 0.25 Gyr older. Although this age estimate agrees with the age coming from the classical turn-off method (t = 11.0 Gyr), its uncertainty is a factor ~3 better, since it avoids systematics in reddening, distance assumptions, and photometric zero point determination. The final absolute age indicates that NGC 2808 is slightly younger than other Galactic globular clusters with similar metallicity. Tables of the photometry are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/586/A51

  2. An Improved Bandstrength Index for the CH G Band of Globular Cluster Giants

    NASA Astrophysics Data System (ADS)

    Martell, Sarah L.; Smith, Graeme H.; Briley, Michael M.

    2008-08-01

    Spectral indices are useful tools for quantifying the strengths of features in moderate-resolution spectra and relating them to intrinsic stellar parameters. This paper focuses on the 4300 Å CH G-band, a classic example of a feature interpreted through use of spectral indices. G-band index definitions, as applied to globular clusters of different metallicity, abound in the literature, and transformations between the various systems, or comparisons between different authors' work, are difficult and not always useful. We present a method for formulating an optimized G-band index, using a large grid of synthetic spectra. To make our new index a reliable measure of carbon abundance, we minimize its dependence on [N/Fe] and simultaneously maximize its sensitivity to [C/Fe]. We present a definition for the new index S2(CH), along with estimates of the errors inherent in using it for [C/Fe] determination, and conclude that it is valid for use with spectra of bright globular cluster red giants over a large range in [Fe/H], [C/Fe], and [N/Fe].

  3. Drug Transporters and Na+/H+ Exchange Regulatory Factor PSD-95/Drosophila Discs Large/ZO-1 Proteins

    PubMed Central

    Walsh, Dustin R.; Nolin, Thomas D.

    2015-01-01

    Drug transporters govern the absorption, distribution, and elimination of pharmacologically active compounds. Members of the solute carrier and ATP binding-cassette drug transporter family mediate cellular drug uptake and efflux processes, thereby coordinating the vectorial movement of drugs across epithelial barriers. To exert their physiologic and pharmacological function in polarized epithelia, drug transporters must be targeted and stabilized to appropriate regions of the cell membrane (i.e., apical versus basolateral). Despite the critical importance of drug transporter membrane targeting, the mechanisms that underlie these processes are largely unknown. Several clinically significant drug transporters possess a recognition sequence that binds to PSD-95/Drosophila discs large/ZO-1 (PDZ) proteins. PDZ proteins, such as the Na+/H+ exchanger regulatory factor (NHERF) family, act to stabilize and organize membrane targeting of multiple transmembrane proteins, including many clinically relevant drug transporters. These PDZ proteins are normally abundant at apical membranes, where they tether membrane-delimited transporters. NHERF expression is particularly high at the apical membrane in polarized tissue such as intestinal, hepatic, and renal epithelia, tissues important to drug disposition. Several recent studies have highlighted NHERF proteins as determinants of drug transporter function secondary to their role in controlling membrane abundance and localization. Mounting evidence strongly suggests that NHERF proteins may have clinically significant roles in pharmacokinetics and pharmacodynamics of several pharmacologically active compounds and may affect drug action in cancer and chronic kidney disease. For these reasons, NHERF proteins represent a novel class of post-translational mediators of drug transport and novel targets for new drug development. PMID:26092975

  4. Systematic Analysis of Bacterial Effector-Postsynaptic Density 95/Disc Large/Zonula Occludens-1 (PDZ) Domain Interactions Demonstrates Shigella OspE Protein Promotes Protein Kinase C Activation via PDLIM Proteins*

    PubMed Central

    Yi, Chae-ryun; Allen, John E.; Russo, Brian; Lee, Soo Young; Heindl, Jason E.; Baxt, Leigh A.; Herrera, Bobby Brooke; Kahoud, Emily; MacBeath, Gavin; Goldberg, Marcia B.

    2014-01-01

    Diseases caused by many Gram-negative bacterial pathogens depend on the activities of bacterial effector proteins that are delivered into eukaryotic cells via specialized secretion systems. Effector protein function largely depends on specific subcellular targeting and specific interactions with cellular ligands. PDZ domains are common domains that serve to provide specificity in protein-protein interactions in eukaryotic systems. We show that putative PDZ-binding motifs are significantly enriched among effector proteins delivered into mammalian cells by certain bacterial pathogens. We use PDZ domain microarrays to identify candidate interaction partners of the Shigella flexneri effector proteins OspE1 and OspE2, which contain putative PDZ-binding motifs. We demonstrate in vitro and in cells that OspE proteins interact with PDLIM7, a member of the PDLIM family of proteins, which contain a PDZ domain and one or more LIM domains, protein interaction domains that participate in a wide variety of functions, including activation of isoforms of protein kinase C (PKC). We demonstrate that activation of PKC during S. flexneri infection is attenuated in the absence of PDLIM7 or OspE proteins and that the OspE PDZ-binding motif is required for wild-type levels of PKC activation. These results are consistent with a model in which binding of OspE to PDLIM7 during infection regulates the activity of PKC isoforms that bind to the PDLIM7 LIM domain. PMID:25124035

  5. Systematic analysis of bacterial effector-postsynaptic density 95/disc large/zonula occludens-1 (PDZ) domain interactions demonstrates Shigella OspE protein promotes protein kinase C activation via PDLIM proteins.

    PubMed

    Yi, Chae-ryun; Allen, John E; Russo, Brian; Lee, Soo Young; Heindl, Jason E; Baxt, Leigh A; Herrera, Bobby Brooke; Kahoud, Emily; MacBeath, Gavin; Goldberg, Marcia B

    2014-10-24

    Diseases caused by many Gram-negative bacterial pathogens depend on the activities of bacterial effector proteins that are delivered into eukaryotic cells via specialized secretion systems. Effector protein function largely depends on specific subcellular targeting and specific interactions with cellular ligands. PDZ domains are common domains that serve to provide specificity in protein-protein interactions in eukaryotic systems. We show that putative PDZ-binding motifs are significantly enriched among effector proteins delivered into mammalian cells by certain bacterial pathogens. We use PDZ domain microarrays to identify candidate interaction partners of the Shigella flexneri effector proteins OspE1 and OspE2, which contain putative PDZ-binding motifs. We demonstrate in vitro and in cells that OspE proteins interact with PDLIM7, a member of the PDLIM family of proteins, which contain a PDZ domain and one or more LIM domains, protein interaction domains that participate in a wide variety of functions, including activation of isoforms of protein kinase C (PKC). We demonstrate that activation of PKC during S. flexneri infection is attenuated in the absence of PDLIM7 or OspE proteins and that the OspE PDZ-binding motif is required for wild-type levels of PKC activation. These results are consistent with a model in which binding of OspE to PDLIM7 during infection regulates the activity of PKC isoforms that bind to the PDLIM7 LIM domain.

  6. Robust classification of protein variation using structural modelling and large-scale data integration.

    PubMed

    Baugh, Evan H; Simmons-Edler, Riley; Müller, Christian L; Alford, Rebecca F; Volfovsky, Natalia; Lash, Alex E; Bonneau, Richard

    2016-04-01

    Existing methods for interpreting protein variation focus on annotating mutation pathogenicity rather than detailed interpretation of variant deleteriousness and frequently use only sequence-based or structure-based information. We present VIPUR, a computational framework that seamlessly integrates sequence analysis and structural modelling (using the Rosetta protein modelling suite) to identify and interpret deleterious protein variants. To train VIPUR, we collected 9477 protein variants with known effects on protein function from multiple organisms and curated structural models for each variant from crystal structures and homology models. VIPUR can be applied to mutations in any organism's proteome with improved generalized accuracy (AUROC .83) and interpretability (AUPR .87) compared to other methods. We demonstrate that VIPUR's predictions of deleteriousness match the biological phenotypes in ClinVar and provide a clear ranking of prediction confidence. We use VIPUR to interpret known mutations associated with inflammation and diabetes, demonstrating the structural diversity of disrupted functional sites and improved interpretation of mutations associated with human diseases. Lastly, we demonstrate VIPUR's ability to highlight candidate variants associated with human diseases by applying VIPUR to de novo variants associated with autism spectrum disorders. PMID:26926108

  7. Robust classification of protein variation using structural modelling and large-scale data integration

    PubMed Central

    Baugh, Evan H.; Simmons-Edler, Riley; Müller, Christian L.; Alford, Rebecca F.; Volfovsky, Natalia; Lash, Alex E.; Bonneau, Richard

    2016-01-01

    Existing methods for interpreting protein variation focus on annotating mutation pathogenicity rather than detailed interpretation of variant deleteriousness and frequently use only sequence-based or structure-based information. We present VIPUR, a computational framework that seamlessly integrates sequence analysis and structural modelling (using the Rosetta protein modelling suite) to identify and interpret deleterious protein variants. To train VIPUR, we collected 9477 protein variants with known effects on protein function from multiple organisms and curated structural models for each variant from crystal structures and homology models. VIPUR can be applied to mutations in any organism's proteome with improved generalized accuracy (AUROC .83) and interpretability (AUPR .87) compared to other methods. We demonstrate that VIPUR's predictions of deleteriousness match the biological phenotypes in ClinVar and provide a clear ranking of prediction confidence. We use VIPUR to interpret known mutations associated with inflammation and diabetes, demonstrating the structural diversity of disrupted functional sites and improved interpretation of mutations associated with human diseases. Lastly, we demonstrate VIPUR's ability to highlight candidate variants associated with human diseases by applying VIPUR to de novo variants associated with autism spectrum disorders. PMID:26926108

  8. Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography

    PubMed Central

    Collins, Marcus D.; Quillin, Michael L.; Hummer, Gerhard; Matthews, Brian W.; Gruner, Sol M.

    2007-01-01

    Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded states. To gain a more complete picture requires that we perturb these structures in a continuous manner, something mutagenesis cannot achieve. With high pressure crystallographic methods it is now possible to explore the detailed properties of proteins while continuously varying thermodynamic parameters. In this paper, we detail the structural response of the cavity-containing mutant L99A of T4 lysozyme, as well as its pseudo wild-type (WT*) counterpart, to hydrostatic pressure. Surprisingly, the cavity has almost no effect on the pressure response: virtually the same changes are observed in WT* as in L99A under pressure. The cavity is most rigid, while other regions deform substantially. This implies that while some residues may increase the thermodynamic stability of a protein, they may also be structurally irrelevant. As recently shown, the cavity fills with water at pressures above 100 MPa while retaining its overall size. The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone. PMID:17292912

  9. DNA binding fluorescent proteins for the direct visualization of large DNA molecules

    PubMed Central

    Lee, Seonghyun; Oh, Yeeun; Lee, Jungyoon; Choe, Sojeong; Lim, Sangyong; Lee, Hyun Soo; Jo, Kyubong; Schwartz, David C.

    2016-01-01

    Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely ‘paints’ entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells. PMID:26264666

  10. Shifting transition states in the unfolding of a large ankyrin repeat protein

    PubMed Central

    Werbeck, Nicolas D.; Rowling, Pamela J. E.; Chellamuthu, Vasuki R.; Itzhaki, Laura S.

    2008-01-01

    The 33-amino-acid ankyrin motif comprises a β-turn followed by two anti-parallel α-helices and a loop and tandem arrays of the motif pack in a linear fashion to produce elongated structures characterized by short-range interactions. In this article we use site-directed mutagenesis to investigate the kinetic unfolding mechanism of D34, a 426-residue, 12-ankyrin repeat fragment of the protein ankyrinR. The data are consistent with a model in which the N-terminal half of the protein unfolds first by unraveling progressively from the start of the polypeptide chain to form an intermediate; in the next step, the C-terminal half of the protein unfolds via two pathways whose transition states have either the early or the late C-terminal ankyrin repeats folded. We conclude that the two halves of the protein unfold by different mechanisms because the N-terminal moiety folds and unfolds in the context of a folded C-terminal moiety, which therefore acts as a “seed” and confers a unique directionality on the process, whereas the C-terminal moiety folds and unfolds in the context of an unfolded N-terminal moiety and therefore behaves like a single-domain ankyrin repeat protein, having a high degree of symmetry and consequently more than one unfolding pathway accessible to it. PMID:18632570

  11. Single-Molecule Analysis of Protein Large-Amplitude Conformational Transitions

    NASA Astrophysics Data System (ADS)

    Yang, Haw

    2011-03-01

    Proteins have evolved to harness thermal fluctuations, rather than frustrated by them, to carry out chemical transformations and mechanical work. What are, then, the operation and design principles of protein machines? To frame the problem in a tractable way, several basic questions have been formulated to guide the experimental design: (a) How many conformational states can a protein sample on the functionally important timescale? (b) What are the inter-conversion rates between states? (c) How do ligand binding or interactions with other proteins modulate the motions? (d) What are the structural basis of flexibility and its underlying molecular mechanics? Guided by this framework, we have studied protein tyrosine phosphatase B, PtpB, from M. tuberculosis (a virulence factor of tuberculosis and a potential drug target) and adenylate kinase, AK, from E. coli (a ubiquitous energy-balancing enzyme in cells). These domain movements have been followed in real time on their respective catalytic timescales using high-resolution single-molecule Förster resonance energy transfer (FRET) spectroscopy. It is shown quantitatively that both PtpB and AK are capable of dynamically sampling two distinct states that correlate well with those observed by x-ray crystallography. Integrating these microscopic dynamics into macroscopic kinetics allows us to place the experimentally measured free-energy landscape in the context of enzymatic turnovers.

  12. Comparative Large Scale Characterization of Plant versus Mammal Proteins Reveals Similar and Idiosyncratic N-α-Acetylation Features*

    PubMed Central

    Bienvenut, Willy V.; Sumpton, David; Martinez, Aude; Lilla, Sergio; Espagne, Christelle; Meinnel, Thierry; Giglione, Carmela

    2012-01-01

    N-terminal modifications play a major role in the fate of proteins in terms of activity, stability, or subcellular compartmentalization. Such modifications remain poorly described and badly characterized in proteomic studies, and only a few comparison studies among organisms have been made available so far. Recent advances in the field now allow the enrichment and selection of N-terminal peptides in the course of proteome-wide mass spectrometry analyses. These targeted approaches unravel as a result the extent and nature of the protein N-terminal modifications. Here, we aimed at studying such modifications in the model plant Arabidopsis thaliana to compare these results with those obtained from a human sample analyzed in parallel. We applied large scale analysis to compile robust conclusions on both data sets. Our data show strong convergence of the characterized modifications especially for protein N-terminal methionine excision, co-translational N-α-acetylation, or N-myristoylation between animal and plant kingdoms. Because of the convergence of both the substrates and the N-α-acetylation machinery, it was possible to identify the N-acetyltransferases involved in such modifications for a small number of model plants. Finally, a high proportion of nuclear-encoded chloroplast proteins feature post-translational N-α-acetylation of the mature protein after removal of the transit peptide. Unlike animals, plants feature in a dedicated pathway for post-translational acetylation of organelle-targeted proteins. The corresponding machinery is yet to be discovered. PMID:22223895

  13. The “Globularization Hypothesis” of the Language-ready Brain as a Developmental Frame for Prosodic Bootstrapping Theories of Language Acquisition

    PubMed Central

    Irurtzun, Aritz

    2015-01-01

    In recent research (Boeckx and Benítez-Burraco, 2014a,b) have advanced the hypothesis that our species-specific language-ready brain should be understood as the outcome of developmental changes that occurred in our species after the split from Neanderthals-Denisovans, which resulted in a more globular braincase configuration in comparison to our closest relatives, who had elongated endocasts. According to these authors, the development of a globular brain is an essential ingredient for the language faculty and in particular, it is the centrality occupied by the thalamus in a globular brain that allows its modulatory or regulatory role, essential for syntactico-semantic computations. Their hypothesis is that the syntactico-semantic capacities arise in humans as a consequence of a process of globularization, which significantly takes place postnatally (cf. Neubauer et al., 2010). In this paper, I show that Boeckx and Benítez-Burraco's hypothesis makes an interesting developmental prediction regarding the path of language acquisition: it teases apart the onset of phonological acquisition and the onset of syntactic acquisition (the latter starting significantly later, after globularization). I argue that this hypothesis provides a developmental rationale for the prosodic bootstrapping hypothesis of language acquisition (cf. i.a. Gleitman and Wanner, 1982; Mehler et al., 1988, et seq.; Gervain and Werker, 2013), which claim that prosodic cues are employed for syntactic parsing. The literature converges in the observation that a large amount of such prosodic cues (in particular, rhythmic cues) are already acquired before the completion of the globularization phase, which paves the way for the premises of the prosodic bootstrapping hypothesis, allowing babies to have a rich knowledge of the prosody of their target language before they can start parsing the primary linguistic data syntactically. PMID:26696916

  14. Trazando la materia oscura con cúmulos globulares

    NASA Astrophysics Data System (ADS)

    Forte, J. C.

    Se describe la estrategia adoptada para mapear la distribución de materia oscura y bariónica en galaxias elípticas cuyos cúmulos globulares están siendo observados con los telescopios VLT y Gemini. Se ejemplifican los resultados con los datos obtenidos en el cúmulo de Fornax.

  15. BVRI CCD photometry of the globular cluster NGC 2808

    SciTech Connect

    Alcaino, G.; Liller, W.; Alvarado, F.; Wenderoth, E. )

    1990-03-01

    As a part of a continuing program, CCD color-magnitude diagrams are presented for the bright globular cluster NGC 2808 in the four colors comprising BVRI. From a comparison of four different CMDs with theoretical isochrones, an age of 16 + or - 2 Gyr is obtained, assuming a value for Fe/H near -1.3. 28 refs.

  16. The optical structure of X-ray globular clusters

    NASA Technical Reports Server (NTRS)

    Hertz, P.; Grindlay, J. E.

    1985-01-01

    CTIO 4-m prime-focus plates of eight globular clusters containing bright X-ray sources have been obtained. Plates in several colors (principally U and B) of each cluster have been digitized. A maximum symmetry method for determining the center of a globular cluster image is described and applied to each cluster in order to determine the cluster center with an accuracy of above 1.0 arc sec. Surface brightness profiles have been derived for seven clusters and fitted with King (1966, 1980) models to yield core radii within about 10 percent. These determinations of the cluster centers and core radii are sufficiently accurate to allow Grindlay et al. (1984) to statistically measure the mass of the globular cluster X-ray sources. Two clusters (NGC 6624 and M15) show significant excesses of light in their cores over the best-fit King model, in agreement with the results of Djorgovski and King (1984). The significance of these excesses, as well as the lack of any dependence of globular cluster structural parameters on color, is discussed.

  17. Possible systematic decreases in the age of globular clusters

    SciTech Connect

    Shi, X.; Schramm, D. N.; Dearborn, D. S.P.; Truran, J. W.

    1994-03-01

    The ages of globular clusters inferred from observations depends sensitively on assumptions like the initial helium abundance and the mass loss rate. A high helium abundance (e.g., Y\\approx0.28) or a mass loss rate of \\sim10^{-11}M_\\odot yr^{-1} near the main sequence turn-off region lowers the current age estimate from 14 Gyr to about 10--12 Gyr, significantly relaxing the constraints on the Hubble constant, allowing values as high as 60km/sec/Mpc for a universe with the critical density and 90km/sec/Mpc for a baryon-only universe. Possible mechanisms for the helium enhancement in globular clusters are discussed, as are arguments for an instability strip induced mass loss near the turn-off. Ages lower than 10 Gyr are not possible even with the operation of both of these mechanisms unless the initial helium abundance in globular clusters is >0.30, which would conflict with indirect measurements of helium abundances in globular clusters.

  18. Globular cluster clustering and tidal features around ultra-compact dwarf galaxies in the halo of NGC 1399

    NASA Astrophysics Data System (ADS)

    Voggel, Karina; Hilker, Michael; Richtler, Tom

    2016-02-01

    We present a novel approach to constrain the formation channels of ultra-compact dwarf galaxies (UCDs). They most probably are an inhomogeneous class of objects, composed of remnants of tidally stripped dwarf elliptical galaxies and star clusters that occupy the high mass end of the globular cluster luminosity function. We use three methods to unravel their nature: 1) we analyzed their surface brightness profiles; 2) we carried out a direct search for tidal features around UCDs; and 3) we compared the spatial distribution of GCs and UCDs in the halo of their host galaxy. Based on FORS2 observations under excellent seeing conditions, we studied the detailed structural composition of a large sample of 97 UCDs in the halo of NGC 1399, the central galaxy of the Fornax cluster, by analyzing their surface brightness profiles. We found that 13 of the UCDs were resolved above the resolution limit of 23 pc and we derived their structural parameters fitting a single Sérsic function. When decomposing their profiles into composite King and Sérsic profiles, we find evidence for faint stellar envelopes at μ = ~ 26 mag arcsec-2, surrounding the UCDs up to an extension of 90 pc in radius. We also show new evidence for faint asymmetric structures and tidal tail-like features surrounding several of these UCDs, a possible tracer of their origin and assembly history within their host galaxy halos. In particular, we present evidence for the first discovery of a significant tidal tail with an extension of ~350 pc around UCD-FORS 2. Finally, we studied the local overdensities in the spatial distribution of globular clusters within the halo of NGC 1399 out to 110 kpc to see if they are related to the positions of the UCDs. We found a local overabundance of globular clusters on a scale of ≤1 kpc around UCDs, when we compared it to the distribution of globulars from the host galaxy. This effect is strongest for the metal-poor blue GCs. We discuss how likely it is that these clustered

  19. Large protein analysis of Staphylococcus aureus and Escherichia coli by MALDI TOF mass spectrometry using amoxicillin functionalized magnetic nanoparticles.

    PubMed

    Hasan, Nazim; Guo, Zhongxian; Wu, Hui-Fen

    2016-09-01

    Bacteria or their protein and peptide entity enrichment using biomolecules-functionalized magnetic nanoparticles, and analysis by matrix assisted laser desorption/ionization mass spectrometry (MALDI MS) is a promising technique to analyze microorganisms. High and low molecular weight proteins like penicillin-binding proteins are responsible for final step synthesis of peptidoglycan biosynthesis; those are the target of lactam antibiotics. In this paper, we synthesized magnetic nanoparticles (mag-NPs) and further modified them with 3-aminopropyltriethoxysilane, and then the β-lactam antibiotic amoxicillin was covalently linked to their surface. β-Lactam group attributes as penicillin binding proteins (PBPs) in bacteria. Staphylococcus aureus and Escherichia coli were used as model bacteria for enrichment based on the β-lactam affinity of magnetic nanoparticles, and then the bacteria were easily separated by an external magnet. Several high molecular weight penicillin binding proteins (PBPs) were detected by MALDI MS containing 10(4) and 10(3) colony-forming unit (cfu) per milileter (mL) of S. aureus and E. coli, respectively. In the case of E. coli, higher molecular weight PBPs were observed at 20 to 55 kDa in MALDI mass spectra. However, S. aureus bacteria resulted with femAB operon-based proteins, with molecular weight of 49570.4 Da, by MALDI MS after using amoxicillin functionalized-mag-NPs. The current approach provides an effective bacteria detection and preconcentration method that has high potential in the near future for fast and sensitive diagnosis of pathogenic bacteria infection. Graphical Abstract Schematic for large proteins analysis by MALDI TOF MS (a) mag-NPs and bacterial interaction (b) Penicillin binding proteins trapping by Amox-mag-NPs. PMID:27565791

  20. Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage

    PubMed Central

    Kenyon, Laura J.; Sabree, Zakee L.

    2014-01-01

    Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, are factors that lead to genome reduction. Size reductions in individual genes due to small-scale deletions have also been implicated in contributing to overall genome shrinkage. Conserved protein functional domains are expected to exhibit low tolerance for mutations and therefore remain relatively unchanged throughout protein length reduction while nondomain regions, presumably under less selective pressures, would shorten. This hypothesis was tested using orthologous protein sets from the Flavobacteriaceae (phylum: Bacteroidetes) and Enterobacteriaceae (subphylum: Gammaproteobacteria) families, each of which includes some of the smallest known genomes. Upon examination of protein, functional domain, and nondomain region lengths, we found that proteins were not uniformly shrinking with genome reduction, but instead increased length variability and variability was observed in both the functional domain and nondomain regions. Additionally, as complete gene loss also contributes to overall genome shrinkage, we found that the largest proteins in the proteomes of nonhost-restricted bacteroidetial and gammaproteobacterial species often were inferred to be involved in secondary metabolic processes, extracellular sensing, or of unknown function. These proteins were absent in the proteomes of obligate insect endosymbionts. Therefore, loss of genes encoding large proteins not required for host-restricted lifestyles in obligate endosymbiont proteomes likely contributes to extreme genome reduction to a greater degree than gene shrinkage. PMID:24671745

  1. Ellipticals with Kinematically Distinct Cores: WFPC2 Imaging of Globular Clusters

    NASA Astrophysics Data System (ADS)

    Forbes, Duncan A.; Franx, Marijn; Illingworth, Garth D.; Carollo, C. M.

    1996-08-01

    New globular clusters may form in the merger of two galaxies. Perhaps the best examples of merger remnants are the set of ellipticals with kinematically distinct cores. Here we present Hubble Space Telescope (HST) Wide Field and Planetary Camera 2 (WFPC2) imaging of 14 kinematically distinct core ellipticals to examine their globular cluster systems. In particular, we probe the galaxy central regions, for which we might expect to see the strongest signatures of some formation and destruction processes. These data increase substantially the number of extragalactic globular cluster systems studied to date. We have developed a method for galaxy subtraction and selection of globular clusters which results in about 200 globulars per galaxy to a limiting magnitude of V ~ 25. Simulations of artificial globulars are described also. We find that the globular cluster luminosity, and color, vary only weakly, if at all, with galactocentric distance. The mean colors of globular clusters are constant with globular cluster magnitude. Several clear trends are also present. First, globular cluster colors are bluer (more metal poor by ~0.5 dex) than the underlying galaxy starlight at any given galactocentric distance. Second, we find a good correlation over roughly 10 magnitudes between the mean globular cluster metallicity and parent galaxy luminosity of the form Z is proportional to L^0.4^. This relationship includes dwarf ellipticals, spiral galaxy bulges, and giant ellipticals. Third, we find that globular cluster surface density distribution can be described by a core model, for which the core radius correlates with galaxy luminosity. Last, for the sample as a whole, the globular cluster systems are closely aligned with the galaxy major axis and are slightly rounder than the galaxy itself, although their are some notable exceptions. Our results favor scenarios in which ellipticals form from massive, gas rich progenitors at early epochs. Detailed simulations of the formation of

  2. Hubble Space Telescope Observations of cD Galaxies and Their Globular Cluster Systems

    NASA Astrophysics Data System (ADS)

    Jordán, Andrés; Côté, Patrick; West, Michael J.; Marzke, Ronald O.; Minniti, Dante; Rejkuba, Marina

    2004-01-01

    We have used WFPC2 on the Hubble Space Telescope (HST) to obtain F450W and F814W images of four cD galaxies (NGC 541 in Abell 194, NGC 2832 in Abell 779, NGC 4839 in Abell 1656, and NGC 7768 in Abell 2666) in the range 5400 km s-1<~cz<~8100 km s-1. For NGC 541, the HST data are supplemented by ground-based B and I images obtained with FORS1 on the Very Large Telescope. We present surface brightness and color profiles for each of the four galaxies, confirming their classification as cD galaxies. Isophotal analyses reveal the presence of subarcsecond-scale dust disks in the nuclei of NGC 541 and NGC 7768. Despite the extreme nature of these galaxies in terms of spatial extent and luminosity, our analysis of their globular cluster (GC) systems reveals no anomalies in terms of specific frequencies, metallicity gradients, average metallicities, or the metallicity offset between the globular clusters and the host galaxy. We show that the latter offset appears roughly constant at Δ[Fe/H]~0.8 dex for early-type galaxies spanning a luminosity range of roughly 4 orders of magnitude. We combine the globular cluster metallicity distributions with an empirical technique described in a series of earlier papers to investigate the form of the protogalactic mass spectrum in these cD galaxies. We find that the observed GC metallicity distributions are consistent with those expected if cD galaxies form through the cannibalism of numerous galaxies and protogalactic fragments that formed their stars and globular clusters before capture and disruption. However, the properties of their GC systems suggest that dynamical friction is not the primary mechanism by which these galaxies are assembled. We argue that cD's instead form rapidly, via hierarchical merging, prior to cluster virialization. Based on observations with the NASA/ESA Hubble Space Telescope obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc

  3. High Cadence Photometric Survey of Four Southern Hemisphere Milky Way Globular Clusters

    NASA Astrophysics Data System (ADS)

    Walker, Douglas Kyle; Albrow, Michael

    2015-08-01

    The Milky Way galaxy is surrounded by some 200 compact Globular Cluster (GCs) of stars, containing up to a million stars each. At 13 billion years of age, these globular clusters are almost as old as the universe itself and were born when the first generations of stars and galaxies formed. GCs are dynamical test beds for investigating and proving theories of stellar evolution. A key parameter to understanding the evolution of GCs is the binary fraction of stars contained within a GC. Binary stars are thought to be a controlling factor in globular cluster evolution and provide a unique tool to determine crucial information about a variety of stellar characteristics such as mass, radius and luminosity. In addition to containing binary stars, GCs also harbor a wide variety of variable stars such as RR Lyrae stars and other stellar exotica, such as blue stragglers, cataclysmic variables, and low-mass X-ray binaries. Recently, a potential new class of rapidly pulsating star, hydrogen-rich subdwarf (sdO) pulsators, has been discovered in the Omega Centauri GC. At present, these Hydrogen sdO pulsators have not been detected in any other GC or among the general field star population.This talk will discuss the use of Difference Imaging Algorithms (DIAs) applied to time-series photometry data from the 10m Southern African Large Telescope (SALT) to investigate short period low amplitude variable stars in the GCs: NGC 1904, NGC 2808, NGC 4833 and NGC 5139. We will present results of• Searching for new discoveries in pulsating stars, cataclysmic variables (a white dwarf star accreting material from its companion), BY Draconis stars (rapidly rotating dwarf stars spun up by a binary companion) and contact binary stars (rapidly rotating binaries that are beginning to coalesce)• Comparison analysis of variables across clusters in relation to cluster Main Sequence regions• Determining the fraction of binary stars in the identified GCsSpecific scientific questions that are

  4. A Large Gene Cluster Encoding Several Magnetosome Proteins Is Conserved in Different Species of Magnetotactic Bacteria

    PubMed Central

    Grünberg, Karen; Wawer, Cathrin; Tebo, Bradley M.; Schüler, Dirk

    2001-01-01

    In magnetotactic bacteria, a number of specific proteins are associated with the magnetosome membrane (MM) and may have a crucial role in magnetite biomineralization. We have cloned and sequenced the genes of several of these polypeptides in the magnetotactic bacterium Magnetospirillum gryphiswaldense that could be assigned to two different genomic regions. Except for mamA, none of these genes have been previously reported to be related to magnetosome formation. Homologous genes were found in the genome sequences of M. magnetotacticum and magnetic coccus strain MC-1. The MM proteins identified display homology to tetratricopeptide repeat proteins (MamA), cation diffusion facilitators (MamB), and HtrA-like serine proteases (MamE) or bear no similarity to known proteins (MamC and MamD). A major gene cluster containing several magnetosome genes (including mamA and mamB) was found to be conserved in all three of the strains investigated. The mamAB cluster also contains additional genes that have no known homologs in any nonmagnetic organism, suggesting a specific role in magnetosome formation. PMID:11571158

  5. Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins

    PubMed Central

    Hamaneh, Mehdi Bagheri; Buck, Matthias

    2009-01-01

    A realistic representation of water molecules is important in molecular dynamics simulation of proteins. However, the standard method of solvating biomolecules, i.e. immersing them in a box of water with periodic boundary conditions, is computationally expensive. The primary hydration shell (PHS) method, developed more than a decade ago and implemented in CHARMM, uses only a thin shell of water around the system of interest, and so greatly reduces the computational cost of simulations. Applying the PHS method, especially to larger proteins, revealed that further optimization and a partial reworking was required and here we present several improvements to its performance. The model is applied to systems with different sizes, and both water and protein behaviors are compared with those observed in standard simulations with periodic boundary conditions and, in some cases, with experimental data. The advantages of the modified PHS method over its original implementation are clearly apparent when it is applied to simulating the 82 KD protein Malate Synthase G. PMID:19382175

  6. CASP10-BCL::Fold efficiently samples topologies of large proteins.

    PubMed

    Heinze, Sten; Putnam, Daniel K; Fischer, Axel W; Kohlmann, Tim; Weiner, Brian E; Meiler, Jens

    2015-03-01

    During CASP10 in summer 2012, we tested BCL::Fold for prediction of free modeling (FM) and template-based modeling (TBM) targets. BCL::Fold assembles the tertiary structure of a protein from predicted secondary structure elements (SSEs) omitting more flexible loop regions early on. This approach enables the sampling of conformational space for larger proteins with more complex topologies. In preparation of CASP11, we analyzed the quality of CASP10 models throughout the prediction pipeline to understand BCL::Fold's ability to sample the native topology, identify native-like models by scoring and/or clustering approaches, and our ability to add loop regions and side chains to initial SSE-only models. The standout observation is that BCL::Fold sampled topologies with a GDT_TS score > 33% for 12 of 18 and with a topology score > 0.8 for 11 of 18 test cases de novo. Despite the sampling success of BCL::Fold, significant challenges still exist in clustering and loop generation stages of the pipeline. The clustering approach employed for model selection often failed to identify the most native-like assembly of SSEs for further refinement and submission. It was also observed that for some β-strand proteins model refinement failed as β-strands were not properly aligned to form hydrogen bonds removing otherwise accurate models from the pool. Further, BCL::Fold samples frequently non-natural topologies that require loop regions to pass through the center of the protein.

  7. RETENTION OF STELLAR-MASS BLACK HOLES IN GLOBULAR CLUSTERS

    SciTech Connect

    Morscher, Meagan; Umbreit, Stefan; Farr, Will M.; Rasio, Frederic A. E-mail: s-umbreit@northwestern.edu E-mail: rasio@northwestern.edu

    2013-01-20

    Globular clusters should be born with significant numbers of stellar-mass black holes (BHs). It has been thought for two decades that very few of these BHs could be retained through the cluster lifetime. With masses {approx}10 M{sub Sun }, BHs are {approx}20 times more massive than an average cluster star. They segregate into the cluster core, where they may eventually decouple from the remainder of the cluster. The small-N core then evaporates on a short timescale. This is the so-called Spitzer instability. Here we present the results of a full dynamical simulation of a globular cluster containing many stellar-mass BHs with a realistic mass spectrum. Our Monte Carlo simulation code includes detailed treatments of all relevant stellar evolution and dynamical processes. Our main finding is that old globular clusters could still contain many BHs at present. In our simulation, we find no evidence for the Spitzer instability. Instead, most of the BHs remain well mixed with the rest of the cluster, with only the innermost few tens of BHs segregating significantly. Over the 12 Gyr evolution, fewer than half of the BHs are dynamically ejected through strong binary interactions in the cluster core. The presence of BHs leads to long-term heating of the cluster, ultimately producing a core radius on the high end of the distribution for Milky Way globular clusters (and those of other galaxies). A crude extrapolation from our model suggests that the BH-BH merger rate from globular clusters could be comparable to the rate in the field.

  8. Co-evolution of galactic nuclei and globular cluster systems

    SciTech Connect

    Gnedin, Oleg Y.; Ostriker, Jeremiah P.; Tremaine, Scott

    2014-04-10

    We revisit the hypothesis that dense galactic nuclei are formed from inspiraling globular clusters. Recent advances in the understanding of the continuous formation of globular clusters over cosmic time and the concurrent evolution of the galaxy stellar distribution allow us to construct a simple model that matches the observed spatial and mass distributions of clusters in the Galaxy and the giant elliptical galaxy M87. In order to compare with observations, we model the effects of dynamical friction and dynamical evolution, including stellar mass loss, tidal stripping of stars, and tidal disruption of clusters by the growing galactic nucleus. We find that inspiraling globular clusters form a dense central structure, with mass and radius comparable to the typical values in observed nuclear star clusters (NSCs) in late-type and low-mass early-type galaxies. The density contrast associated with the NSC is less pronounced in giant elliptical galaxies. Our results indicate that the NSC mass as a fraction of mass of the galaxy stellar spheroid scales as M{sub NSC}/M{sub ∗}≈0.0025 M{sub ∗,11}{sup −0.5}. Thus disrupted globular clusters could contribute most of the mass of NSCs in galaxies with stellar mass below 10{sup 11} M {sub ☉}. The inner part of the accumulated cluster may seed the growth of a central black hole via stellar dynamical core collapse, thereby relieving the problem of how to form luminous quasars at high redshift. The seed black hole may reach ∼10{sup 5} M {sub ☉} within ≲ 1 Gyr of the beginning of globular cluster formation.

  9. Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets

    PubMed Central

    Krejci, Adam; Hupp, Ted R.; Lexa, Matej; Vojtesek, Borivoj; Muller, Petr

    2016-01-01

    Motivation: Proteins often recognize their interaction partners on the basis of short linear motifs located in disordered regions on proteins’ surface. Experimental techniques that study such motifs use short peptides to mimic the structural properties of interacting proteins. Continued development of these methods allows for large-scale screening, resulting in vast amounts of peptide sequences, potentially containing information on multiple protein-protein interactions. Processing of such datasets is a complex but essential task for large-scale studies investigating protein-protein interactions. Results: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters. The method was applied on a previously published smaller dataset containing distinct classes of ligands for SH3 domains, as well as on a new, an order of magnitude larger dataset containing epitopes for several monoclonal antibodies. The software successfully identified clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Another test indicates that processing of even much larger datasets is computationally feasible. Availability and implementation: Hammock is published under GNU GPL v. 3 license and is freely available as a standalone program (from http://www.recamo.cz/en/software/hammock-cluster-peptides/) or as a tool for the Galaxy toolbox (from https://toolshed.g2.bx.psu.edu/view/hammock/hammock). The source code can be downloaded from https://github.com/hammock-dev/hammock/releases. Contact: muller@mou.cz Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26342231

  10. Protein crystal growth in microgravity review of large scale temperature induction method: bovine insulin, human insulin and human alpha interferon

    NASA Astrophysics Data System (ADS)

    Long, Marianna M.; Bishop, John Bradford; Nagabhushan, Tattanahalli L.; Reichert, Paul; Smith, G. David; DeLucas, Lawrence J.

    1996-10-01

    The protein crystal growth facility (PCF) is space-flight hardware that accommodates large scale protein crystal growth experiments using temperature change as the inductive step. Recent modifications include specialized instrumentation for monitoring crystal nucleation with laser light scattering. This paper reviews results from the PCF's first seven flights on the Space Shuttle, the last with laser light scattering instrumentation. The PCF's objective is twofold: (1) production of high quality protein crystals for X-ray analysis and subsequent structure based drug design and (2) preparation of a large quantity of relatively contaminant free crystals for use as time-release protein pharmaceuticals. The first three Shuttle flights with bovine insulin constituted the PCF's proof of concept, demonstrating that the space-grown crystals were larger and diffracted to higher resolution than their earth-grown counterparts. The later four PCF missions were used to grow recombinant human insulin crystals for X-ray analysis and to continue productions trials aimed at the development of a processing facility for crystalline recombinant alpha interferon.

  11. Nearby Spiral Galaxy Globular Cluster Systems. II. Globular Cluster Metallicities in NGC 300

    NASA Astrophysics Data System (ADS)

    Nantais, Julie B.; Huchra, John P.; Barmby, Pauline; Olsen, Knut A. G.

    2010-03-01

    We present new metallicity estimates for globular cluster (GC) candidates in the Sd spiral NGC 300, one of the nearest spiral galaxies outside the Local Group. We have obtained optical spectroscopy for 44 Sculptor Group GC candidates with the Boller and Chivens (B&C) spectrograph on the Baade Telescope at Las Campanas Observatory. There are two GCs in NGC 253 and 12 objects in NGC 300 with globular-cluster-like spectral features, nine of which have radial velocities above 0 km s-1. The remaining three, due to their radial velocities being below the expected 95% confidence limit for velocities of NGC 300 halo objects, are flagged as possible foreground stars. The non-cluster-like candidates included 13 stars, 15 galaxies, and an H II region. One GC, four galaxies, two stars, and the H II region from our sample were identified in archival Hubble Space Telescope images. For the GCs, we measure spectral indices and estimate metallicities using an empirical calibration based on Milky Way GCs. The GCs of NGC 300 appear similar to those of the Milky Way. Excluding possible stars and including clusters from the literature, the GC system (GCS) has a velocity dispersion of 68 km s-1 and has no clear evidence of rotation. The mean metallicity for our full cluster sample plus one literature object is [Fe/H] = -0.94, lying above the relationship between mean GC metallicity and overall galaxy luminosity. Excluding the three low-velocity candidates, we obtain a mean [Fe/H] = -0.98, still higher than expected, raising the possibility of significant foreground star contamination even in this sample. Visual confirmation of genuine GCs using high-resolution space-based imagery could greatly reduce the potential problem of interlopers in small samples of GCSs in low-radial-velocity galaxies. Data for this project were obtained at the Baade 6.5 m telescope, Las Campanas Observatory, Chile. This publication makes use of data products from the Two Micron All Sky Survey, which is a joint

  12. PEERING INTO THE CORE OF A GLOBULAR CLUSTER

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Astronomers have used NASA's Hubble Space Telescope to peer into the center of a dense swarm of stars called Omega Centauri. Located some 17,000 light-years from Earth, Omega Centauri is a massive globular star cluster, containing several million stars swirling in locked orbits around a common center of gravity. The stars are packed so densely in the cluster's core that it is difficult for ground-based telescopes to make out individual stars. Hubble's high resolution is able to pick up where ground-based telescopes leave off, capturing distinct points of light from stars at the very center of the cluster. Omega Centauri is so large in our sky that only a small part of it fits within the field of view of the Wide Field and Planetary Camera 2 (WFPC2) on the Hubble Space Telescope. Yet even this tiny patch contains some 50,000 stars, all packed into a region only about 13 light-years wide. For comparison, a similarly sized region centered on the Sun would contain about a half dozen stars. The vast majority of stars in this Hubble image are faint, yellow-white dwarf stars similar to our Sun. The handful of bright yellow-orange stars are red giants that have begun to exhaust their nuclear fuel and have expanded to diameters about a hundred times that of the Sun. A number of faint blue stars are also visible in the image. These are in a brief phase of evolution between the dwarf stage and the red-giant stage, during which the surface temperature is high. The stars in Omega Centauri are all very old, about 12 billion years. Stars with a mass as high as that of our Sun have already completed their evolution and have faded away as white dwarfs, too faint to be seen even in the Hubble image. The stars in the core of Omega Centauri are so densely packed that occasionally one of them will actually collide with another one. Even in the dense center of Omega Centauri, stellar collisions will be infrequent. But the cluster is so old that many thousands of collisions have occurred

  13. Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins.

    PubMed

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

    2016-01-29

    Pseudocontact shifts (PCSs) induced by paramagnetic lanthanides produce pronounced effects in nuclear magnetic resonance spectra, which are easily measured and which deliver valuable long-range structure restraints. Even sparse PCS data greatly enhance the success rate of 3D (3-dimensional) structure predictions of proteins by the modeling program Rosetta. The present work extends this approach to 3D structures of larger proteins, comprising more than 200 residues, which are difficult to model by Rosetta without additional experimental restraints. The new algorithm improves the fragment assembly method of Rosetta by utilizing PCSs generated from paramagnetic lanthanide ions attached at four different sites as the only experimental restraints. The sparse PCS data are utilized at multiple stages, to identify native-like local structures, to rank the best structural models and to rebuild the fragment libraries. The fragment libraries are refined iteratively until convergence. The PCS-driven iterative resampling algorithm is strictly data dependent and shown to generate accurate models for a benchmark set of eight different proteins, ranging from 100 to 220 residues, using solely PCSs of backbone amide protons.

  14. Distribution of circular proteins in plants: large-scale mapping of cyclotides in the Violaceae

    PubMed Central

    Burman, Robert; Yeshak, Mariamawit Y.; Larsson, Sonny; Craik, David J.; Rosengren, K. Johan; Göransson, Ulf

    2015-01-01

    During the last decade there has been increasing interest in small circular proteins found in plants of the violet family (Violaceae). These so-called cyclotides consist of a circular chain of approximately 30 amino acids, including six cysteines forming three disulfide bonds, arranged in a cyclic cystine knot (CCK) motif. In this study we map the occurrence and distribution of cyclotides throughout the Violaceae. Plant material was obtained from herbarium sheets containing samples up to 200 years of age. Even the oldest specimens contained cyclotides in the preserved leaves, with no degradation products observable, confirming their place as one of the most stable proteins in nature. Over 200 samples covering 17 of the 23–31 genera in Violaceae were analyzed, and cyclotides were positively identified in 150 species. Each species contained a unique set of between one and 25 cyclotides, with many exclusive to individual plant species. We estimate the number of different cyclotides in the Violaceae to be 5000–25,000, and propose that cyclotides are ubiquitous among all Violaceae species. Twelve new cyclotides from six phylogenetically dispersed genera were sequenced. Furthermore, the first glycosylated derivatives of cyclotides were identified and characterized, further increasing the diversity and complexity of this unique protein family. PMID:26579135

  15. Constraints on helium enhancement in the globular cluster M4 (NGC 6121): The horizontal branch test

    SciTech Connect

    Valcarce, A. A. R.; De Medeiros, J. R.; Catelan, M.; Alonso-García, J.; Cortés, C.

    2014-02-20

    Recent pieces of evidence have revealed that most, and possibly all, globular star clusters are composed of groups of stars that formed in multiple episodes with different chemical compositions. In this sense, it has also been argued that variations in the initial helium abundance (Y) from one population to the next are also the rule, rather than the exception. In the case of the metal-intermediate globular cluster M4 (NGC 6121), recent high-resolution spectroscopic observations of blue horizontal branch (HB) stars (i.e., HB stars hotter than the RR Lyrae instability strip) suggest that a large fraction of blue HB stars are second-generation stars formed with high helium abundances. In this paper, we test this scenario by using recent photometric and spectroscopic data together with theoretical evolutionary computations for different Y values. Comparing the photometric data with the theoretically derived color-magnitude diagrams, we find that the bulk of the blue HB stars in M4 have ΔY ≲ 0.01 with respect to the cluster's red HB stars (i.e., HB stars cooler than the RR Lyrae strip)—a result which is corroborated by comparison with spectroscopically derived gravities and temperatures, which also favor little He enhancement. However, the possible existence of a minority population on the blue HB of the cluster with a significant He enhancement level is also discussed.

  16. Globular Clusters, Ultra-Compact Dwarfs, and the Formation of Galaxy Halos

    NASA Astrophysics Data System (ADS)

    Peng, Eric

    2015-08-01

    Globular clusters (GCs) are a distinctive and ubiquitous constituent of galaxy halos. Their existence alludes to an early epoch of galaxy building characterized by the high star formation rates needed to form massive clusters, and a merging process that produced the extended, spheroidal stellar halos in today's galaxies. While studies of stellar halos are generally limited by low surface brightnesses or the faintness of individual halo stars, GCs are bright and compact, making them excellent tracers of stellar halos out to hundreds of megaparsecs. The Next Generation Virgo Cluster Survey (NGVS) is a CFHT Large Program that has acquired imaging of the 104 square degrees within the Virgo Cluster's virial radius. This deep and contiguous imaging of the nearest galaxy cluster provides us a new view of globular clusters across the full range of galaxy morphology and mass, as well as in the regions between galaxies. It also provides the first complete census of ultra-compact dwarfs (UCDs) in Virgo, objects which may be related to massive GCs and galaxy nuclei. In this talk, I will present what we have learned so far about extragalactic GC systems and UCDs from the NGVS, from both photometry and spectroscopy.

  17. A spectroscopic study of the Globular Cluster M28 (NGC 6626)

    NASA Astrophysics Data System (ADS)

    Villanova, S.; Moni Bidin, C.; Mauro, F.; Munoz, C.; Monaco, L.

    2016-10-01

    We present the abundance analysis for a sample of 17 red giant branch stars in the metal-poor globular cluster M28 based on high resolution spectra. This is the first extensive spectroscopic study of this cluster. We derive abundances of O, Na, Mg, Al, Si, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Ba, La, Ce, and Eu. We find a metallicity of [Fe/H]=-1.29±0.01 and an α-enhancement of +0.34±0.01 (errors on the mean), typical of Halo Globular Clusters in this metallicity regime. A large spread is observed in the abundances of light elements O, Na, and Al. Mg also shows an anticorrelation with Al with a significance of 3σ. The cluster shows a Na-O anticorrelation and a Na-Al correlation. This correlation is not linear but "segmented" and that the stars are not distributed continuously, but form at least 3 well separated sub-populations. In this aspect M28 resembles NGC 2808 that was found to host at least 5 sub-populations. The presence of a Mg-Al anticorrelation favor massive AGB stars as the main polluters responsible for the multiple-population phenomenon.

  18. Neutron stars and millisecond pulsars from accretion-induced collapse in globular clusters

    NASA Technical Reports Server (NTRS)

    Bailyn, Charles D.; Grindlay, Jonathan E.

    1990-01-01

    This paper examines the limits on the number of millisecond pulsars which could be formed in globular clusters by the generally accepted scenario (in which a neutron star is created by the supernova of an initially massive star and subsequently captures a companion to form a low-mass X-ray binary which eventually becomes a millisecond pulsar). It is found that, while the number of observed low-mass X-ray binaries can be adequately explained in this way, the reasonable assumption that the pulsar luminosity function in clusters extends below the current observational limits down to the luminosity of the faintest millisecond pulsars in the field suggests a cluster population of millisecond pulsars which is substantially larger than the standard model can produce. Alleviating this problem by postulating much shorter lifetimes for the X-ray binaries requires massive star populations sufficiently large that the mass loss resulting from their evolution would be likely to unbind the cluster. It is argued that neutron star formation in globular clusters by accretion-induced collapse of white dwarfs may resolve the discrepancy in birthrates.

  19. Ultraviolet properties of individual hot stars in globular cluster cores. I - NGC 1904 (M79)

    NASA Technical Reports Server (NTRS)

    Altner, B.; Matilsky, T. A.

    1993-01-01

    As part of an observing program using the IUE satellite to investigate the properties of stars within the cores of Galactic globular clusters, we have obtained three spectra of the cluster NGC 1904 (M79). All three were long-integration-time, short-wavelength (SWP) spectra obtained at the so-called 'center-of-light', and all three showed evidence of multiple sources within the IUE large aperture. We describe the analysis of these spectra and present evidence that the UV sources represent individual hot stars in the post-horizontal-branch stage of evolution. We see more UV-bright objects in the core of this cluster than expected from surveys of similar objects discovered in the outer regions of other globulars, leading us to conclude that dynamical effects in the core may significantly alter the path of evolution off the horizontal branch. The spectra also appear to be fitted more closely by models using Population I metal abundances than by Population II abundance models.

  20. ON THE BIRTH MASSES OF THE ANCIENT GLOBULAR CLUSTERS

    SciTech Connect

    Conroy, Charlie

    2012-10-10

    All globular clusters (GCs) studied to date show evidence for internal (star-to-star) variation in their light-element abundances (including Li, C, N, O, F, Na, Mg, Al, and probably He). These variations have been interpreted as evidence for multiple star formation episodes within GCs, with secondary episodes fueled, at least in part, by the ejecta of asymptotic giant branch (AGB) stars from a first generation of stars. A major puzzle emerging from this otherwise plausible scenario is that the fraction of stars associated with the second episode of star formation is observed to be much larger than expected for a standard initial mass function. The present work investigates this tension by modeling the observed anti-correlation between [Na/Fe] and [O/Fe] for 20 Galactic GCs. If the abundance pattern of the retained AGB ejecta does not depend on GC mass at fixed [Fe/H], then a strong correlation is found between the fraction of current GC stellar mass composed of pure AGB ejecta, f{sub p} , and GC mass. This fraction varies from 0.20 at low masses (10{sup 4.5} M{sub Sun }) to 0.45 at high masses (10{sup 6.5} M{sub Sun }). The fraction of mass associated with pure AGB ejecta is directly related to the total mass of the cluster at birth; the ratio between the initial and present mass in stars can therefore be derived. Assuming a star formation efficiency of 50%, the observed Na-O anti-correlations imply that GCs were at least 10-20 times more massive at birth, a conclusion that is in qualitative agreement with previous work. These factors are lower limits because any mass-loss mechanism that removes first- and second-generation stars equally will leave f{sub p} unchanged. The mass dependence of f{sub p} probably arises because lower mass GCs are unable to retain all of the AGB ejecta from the first stellar generation. Recent observations of elemental abundances in intermediate-age Large Magellanic Cloud clusters are re-interpreted and shown to be consistent with this

  1. Hunting for Optical Companions to Binary Msps in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Ferraro, Francesco

    2009-07-01

    Here we present a proposal which exploits the re-newed potential of HST after the Service Mission 4 for probing the population of binary Millisecond Pulsars {MSPs} in Globular Clusters. In particular we intend to: {1} extend the search for optical counterparts in Terzan 5, by pushing the performance of the WFC3 IR channel to sample the entire MS extension down to M=0.1 Mo; {2} perform a deep multi-band search of MSP companions with the WFC3, in 3 clusters {namely NGC6440, M28 and M5}, where recent radio observations have found particularly interesting objects; {3} derive an accurate radial velocity {with STIS} of the puzzling optical companion COM6266B recently discovered by our group, to firmly a