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Sample records for large globular protein

  1. 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.

  2. 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

  3. 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

  4. 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

  5. How to develop globular proteins into adhesives.

    PubMed

    van der Leeden, M C; Rutten, A A; Frens, G

    2000-05-26

    To make globular proteins suitable for application in adhesives, the specific bonds and interactions which shape their structure have to broken. Only then, a layer of relatively large, flexible and interwoven polymer chains, which are firmly attached to the solid surface by adsorption, can be created. Such a network layer is essential to save the adhesive bond under an applied force, because it can distribute the concentration of stresses generated at the interface into the bulk. Unfolding and swelling of a protein can be achieved by changing the solvent quality. For the globular whey protein beta-lactoglobulin, the optimal conditions for unfolding and swelling is found with 98% formic acid as a solvent. In formic acid, beta-lactoglobulin looses its amphoteric character (it is protonated, probably for approximately 20%). In addition, formic acid is less polar than water and thus a better solvent for the apolar parts of the protein. The swelling and unfolding behaviour of beta-lactoglobulin is studied by viscosity and CD-spectroscopy measurements. For the interpretation of the results we apply the Kuhn formalism that the conformation of a protein can be described in terms of a statistical chain which consists of segments of an average persistence length P. The statistical segment length P, which varies with the experimental conditions, is directly related to the adsorption energy required for a strong adhesion between coil and surface. It determines the depletion energy kT P(-2) m(-2) which must be overcome by specific attraction between side groups of the protein chain and the surface. For beta-lactoglobulin in 98% formic acid, we find a P value of approximately 2.2 nm, pointing at a relatively flexible chain. The minimum net adsorption energy kT P(-2) is then approximately 1 mJ m(-2), a relatively small value to be exceeded. Preliminary results of destructive adhesion tests on beech wood lap-shear joints reveal promising tensile strengths of approximately 2

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

    PubMed Central

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

    2015-01-01

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

  7. Self-Assembly of Globular Protein-Polymer Diblock Copolymers

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  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

    2016-02-01

    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. PMID:26907186

  10. Computational and theoretical studies of globular proteins

    NASA Astrophysics Data System (ADS)

    Pagan, Daniel L.

    Protein crystallization is often achieved in experiment through a trial and error approach. To date, there exists a dearth of theoretical understanding of the initial conditions necessary to promote crystallization. While a better understanding of crystallization will help to create good crystals suitable for structure analysis, it will also allow us to prevent the onset of certain diseases. The core of this thesis is to model and, ultimately, understand the phase behavior of protein particles in solution. Toward this goal, we calculate the fluid-fluid coexistence curve in the vicinity of the metastable critical point of the modified Lennard-Jones potential, where it has been shown that nucleation is increased by many orders of magnitude. We use finite-size scaling techniques and grand canonical Monte Carlo simulation methods. This has allowed us to pinpoint the critical point and subcritical region with high accuracy in spite of the critical fluctuations that hinder sampling using other Monte Carlo techniques. We also attempt to model the phase behavior of the gamma-crystallins, mutations of which have been linked to genetic cataracts. The complete phase behavior of the square well potential at the ranges of attraction lambda = 1.15 and lambda = 1.25 is calculated and compared with that of the gammaII-crystallin. The role of solvent is also important in the crystallization process and affects the phase behavior of proteins in solution. We study a model that accounts for the contribution of the solvent free-energy to the free-energy of globular proteins. This model allows us to model phase behavior that includes solvent.

  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. GlobPlot: exploring protein sequences for globularity and disorder

    PubMed Central

    Linding, Rune; Russell, Robert B.; Neduva, Victor; Gibson, Toby J.

    2003-01-01

    A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Non-globular sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http://globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface—GlobPipe—for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity. PMID:12824398

  13. Correlations between internal mobility and stability of globular proteins.

    PubMed

    Wüthrich, K; Wagner, G; Richarz, R; Braun, W

    1980-10-01

    The recent work is surveyed which leads to the suggestions that the conformation of globular proteins in solution corresponds to a dynamic ensemble of rapidly interconverting spatial structures, that clusters of hydrophobic amino acid side chains have an important role in the architecture of protein molecules, and that mechanistic aspects of protein denaturation can be correlated with internal mobility seen in the native conformation. These conclusions resulted originally from high resolution 1H nuclear magnetic resonance (NMR) studies of aromatic ring mobility, exchange of interior amide protons and thermal denaturation of the basic pancreatic trypsin inhibitor and a group of related proteins. Various new approaches to further characterize proteins in solution have now been taken and preliminary data are presented. These include computer graphics to outline hydrophobic clusters in globular protein structures, high resolution 1H-NMR experiments at variable hydrostatic pressure and 13C-NMR relaxation measurements. At the present early stage of these new investigations it appears that the hydrophobic cluster model for globular proteins is compatible with the data obtained. PMID:7248460

  14. Universal features of fluctuations in globular proteins.

    PubMed

    Erman, Burak

    2016-06-01

    Using data from 2000 non-homologous protein crystal structures, we show that the distribution of residue B factors of proteins collapses onto a single master curve. We show by maximum entropy arguments that this curve is a Gamma function whose order and dispersion are obtained from experimental data. The distribution for any given specific protein can be generated from the master curve by a linear transformation. Any perturbation of the B factor distribution of a protein, imposed at constant energy, causes a decrease in the entropy of the protein relative to that of the reference state. Proteins 2016; 84:721-725. © 2016 Wiley Periodicals, Inc. PMID:26971570

  15. Crystallization of asymmetric patchy models for globular proteins in solution

    NASA Astrophysics Data System (ADS)

    Fusco, Diana; Charbonneau, Patrick

    2013-07-01

    Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near-quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy generally impacts the phase diagram and nucleation dynamics of this family of soft matter models. We find the role of the geometry asymmetry to be weak, but the energy asymmetry to markedly interfere with the crystallization thermodynamics and kinetics. These results provide a rationale for the success and occasional failure of the proposal of George and Wilson for protein crystallization conditions as well as physical guidance for developing more effective protein crystallization strategies.

  16. Modeling repetitive, non-globular proteins.

    PubMed

    Basu, Koli; Campbell, Robert L; Guo, Shuaiqi; Sun, Tianjun; Davies, Peter L

    2016-05-01

    While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here. PMID:26914323

  17. 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

  18. 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

  19. Dynamical theory of activated processes in globular proteins.

    PubMed Central

    Northrup, S H; Pear, M R; Lee, C Y; McCammon, J A; Karplus, M

    1982-01-01

    A method is described for calculating the reaction rate in globular proteins of activated processes such as ligand binding or enzymatic catalysis. The method is based on the determination of the probability that the system is in the transition state and of the magnitude of the reactive flux for transition-state systems. An "umbrella sampling" simulation procedure is outlined for evaluating the transition-state probability. The reactive flux is obtained from an approach described previously for calculating the dynamics of transition-state trajectories. An application to the rotational isomerization of an aromatic ring in the bovine pancreatic trypsin inhibitor is presented. The results demonstrate the feasibility of calculating rate constants for reactions in proteins and point to the importance of solvent effects for reactions that occur near the protein surface. PMID:6955788

  20. Dynamical Theory of Activated Processes in Globular Proteins

    NASA Astrophysics Data System (ADS)

    Northrup, Scott H.; Pear, Michael R.; Lee, Chyuan-Yih; McCammon, J. Andrew; Karplus, Martin

    1982-07-01

    A methos is described for calculating the reaction rate in globular proteins of activated processes such as ligand binding or enzymatic catalysis. The method is based on the determination of the probability that the system is in the transition state and of the magnitude of the reactive flux for transition-state systems. An ``umbrella sampling'' simulation procedure is outlined for evaluating the transition-state probability. The reactive flux is obtained from an approach described previously for calculating the dynamics of transition-state trajectories. An application to the rotational isomerization of an aromatic ring in the bovine pancreatic trypsin inhibitor is presented. The results demonstrate the feasibility of calculating rate constants for reactions in proteins and point to the importance of solvent effects for reactions that occur near the protein surface.

  1. Understanding the folding rates and folding nuclei of globular proteins.

    PubMed

    Finkelstein, Alexei V; Ivankov, Dmitry N; Garbuzynskiy, Sergiy O; Galzitskaya, Oxana V

    2007-12-01

    The first part of this paper contains an overview of protein structures, their spontaneous formation ("folding"), and the thermodynamic and kinetic aspects of this phenomenon, as revealed by in vitro experiments. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" <--> "native state") transition proceeds without accumulation of metastable intermediates, but includes only the unstable "transition state". This state, which is the most unstable in the folding pathway, and its structured core (a "nucleus") are distinguished by their essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of a protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then, we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. Finally, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of the transition state) in reasonable agreement with experimental data. PMID:18220841

  2. Detection of a large-scale structure of intracluster globular clusters in the Virgo cluster.

    PubMed

    Lee, Myung Gyoon; Park, Hong Soo; Hwang, Ho Seong

    2010-04-16

    Globular clusters are usually found in galaxies, and they are excellent tracers of dark matter. Long ago it was suggested that intracluster globular clusters (IGCs) may exist that are bound to a galaxy cluster rather than to any single galaxy. Here we present a map showing the large-scale distribution of globular clusters over the entire Virgo cluster. It shows that IGCs are found out to 5 million light years from the Virgo center and that they are concentrated in several substructures that are much larger than galaxies. These objects might have been mostly stripped off from low-mass dwarf galaxies. PMID:20223950

  3. Unbiased sampling of globular lattice proteins in three dimensions.

    PubMed

    Jacobsen, Jesper Lykke

    2008-03-21

    We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64(3)=262 144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system. PMID:18517831

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. Influence of drying on the secondary structure of intrinsically disordered and globular proteins.

    PubMed

    Hundertmark, Michaela; Popova, Antoaneta V; Rausch, Saskia; Seckler, Robert; Hincha, Dirk K

    2012-01-01

    Circular dichroism (CD) spectroscopy of five Arabidopsis late embryogenesis abundant (LEA) proteins constituting the plant specific families LEA_5 and LEA_6 showed that they are intrinsically disordered in solution and partially fold during drying. Structural predictions were comparable to these results for hydrated LEA_6, but not for LEA_5 proteins. FTIR spectroscopy showed that verbascose, but not sucrose, strongly affected the structure of the dry proteins. The four investigated globular proteins were only mildly affected by drying in the absence, but strongly in the presence of sugars. These data highlight the larger structural flexibility of disordered compared to globular proteins and the impact of sugars on the structure of both disordered and globular proteins during drying. PMID:22155233

  9. Measurement of solvation responses at multiple sites in a globular protein.

    PubMed

    Abbyad, Paul; Shi, Xinghua; Childs, William; McAnaney, Tim B; Cohen, Bruce E; Boxer, Steven G

    2007-07-19

    Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we characterize the solvation kinetics at sites throughout the sequence of a small globular protein, the B1 domain of streptococcal protein G (GB1), using the synthetic fluorescent amino acid Aladan. Aladan was incorporated into seven different GB1 sites, and the time-dependent Stokes shift was measured over the femtosecond to nanosecond time scales by fluorescence upconversion and time-correlated single photon counting. The seven sites range from buried within the protein core to fully solvent-exposed on the protein surface, and are located on different protein secondary structures including beta-sheets, helices, and loops. The dynamics in the protein sites were compared against the free fluorophore in buffer. All protein sites exhibited an initial, ultrafast Stokes shift on the subpicosecond time scale similar to that observed for the free fluorophore, but smaller in magnitude. As the probe is moved from the surface to more buried sites, the dynamics of the solvation response become slower, while no clear correlation between dynamics and secondary structure is observed. We suggest that restricted movements of the surrounding protein residues give rise to the observed long time dynamics and that such movements comprise a large portion of the protein's solvation response. The proper treatment of dynamic Stokes shift data when the time scale for solvation is comparable to the fluorescence lifetime is discussed. PMID:17592867

  10. Measurement of Solvation Responses at Multiple Sites in a Globular Protein

    PubMed Central

    Abbyad, Paul; Shi, Xinghua; Childs, William; McAnaney, Tim B.; Cohen, Bruce E.; Boxer, Steven G.

    2008-01-01

    Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we characterize the solvation kinetics at sites throughout the sequence of a small globular protein, the B1 domain of streptococcal protein G (GB1), using the synthetic fluorescent amino acid Aladan. Aladan was incorporated into seven different GB1 sites, and the time-dependent Stokes shift measured over the femtosecond to nanosecond timescales by fluorescence upconversion and time-correlated single photon counting. The seven sites range from buried within the protein core to fully solvent-exposed on the protein surface, and are located on different protein secondary structures including β-sheets, helices and loops. The dynamics in the protein sites were compared against the free fluorophore in buffer. All protein sites exhibited an initial, ultra-fast Stokes shift on the sub-picosecond timescale similar to that observed for the free fluorophore, but smaller in magnitude. As the probe is moved from the surface to more buried sites, the dynamics of the solvation response become slower, while no clear correlation between dynamics and secondary structure is observed. We suggest that restricted movements of the surrounding protein residues give rise to the observed long time dynamics and that such movements comprise a large portion of the protein’s solvation response. The proper treatment of dynamic Stokes shift data when the timescale for solvation is comparable to the fluorescence lifetime is discussed. PMID:17592867

  11. Canine distemper virus envelope protein interactions modulated by hydrophobic residues in the fusion protein globular head.

    PubMed

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

    2015-01-15

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

  12. 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

  13. 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

  14. 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.

  15. Static structure factor and collective diffusion of globular proteins in concentrated aqueous solution

    NASA Astrophysics Data System (ADS)

    Fine, Bernard M.; Lomakin, Aleksey; Ogun, Olutayo O.; Benedek, George B.

    1996-01-01

    We report our measurement of the time average and the temporal autocorrelation function of the intensity of light scattered by the highly monomeric globular protein, bovine γII-crystallin, in aqueous solution as a function of wave number q, protein volume fraction φ, and temperature T. The time average intensity data is used to obtain the q→0 limit of the static structure factor S(φ,T), as a function of φ and T. We show that S(φ,T) may be well characterized by modeling the proteins as interacting through the Baxter adhesive hard sphere pair interaction potential. The temporal autocorrelation function data is used to determine the collective diffusion coefficient D˜(φ,T) of the proteins as a function of φ and T. We then obtain the experimental hydrodynamic factor H˜(φ,T)≡S(φ,T)[D˜(φ,T)/D0(T)], where D0(T) is the diffusion coefficient of the individual proteins in the φ→0 limit. We find that H˜ exhibits a different φ-dependence at low (φ≤0.016) and high (φ≳0.02) protein volume fractions. In the low φ domain our data for H˜ are consistent with the theoretical result for the collective diffusion in the q→0, t→0 limit. However, for φ≳0.02 we find a deviation from single exponential decay in the autocorrelation functions, and an unexpected, large change in the slope of the H˜ vs φ relation. This crossover at such low φ suggests the existence of a heretofore unappreciated length scale in the dynamics of colloid solutions. Clearly, further theoretical insights are required to understand the origin of this crossover behavior.

  16. Protein cluster formation during enzymatic cross-linking of globular proteins.

    PubMed

    Saricay, Yunus; Dhayal, Surender Kumar; Wierenga, Peter Alexander; de Vries, Renko

    2012-01-01

    Work on enzymatic cross-linking of globular food proteins has mainly focused on food functional effects such as improvements of gelation and enhanced stabilization of emulsions and foams, and on the detailed biochemical characterization of the cross-linking chemistry. What is still lacking is a physical characterization of cluster formation and gelation, as has been done for example, for cluster formation and gelation during heat-induced protein aggregation. Here we present preliminary results along these lines. We propose that enzymatic cross-linking of apo-alpha-lactalbumin is a good model system for studying the problem of cluster formation and gelation during enzymatic cross-linking of globular proteins. We present initial results on cluster sizes produced when crosslinking dilute solutions of apo-alpha-lactalbumin with a range of cross-linking enzymes: microbial transglutaminase, horseradish peroxidase, and mushroom tyrosinase. These results are used to highlight similarities and differences between different enzymes, when acting on the same substrate. Next we consider cluster growth and gelation in somewhat more detail for the specific case of cross-linking by horseradish peroxidase, under the periodic addition of H2O2. Upon increasing the initial concentration of apo-alpha-lactalbumin, at a fixed enzyme-to-substrate ratio and fixed reaction time, the size of the clusters at the end of the reaction increases rapidly, and above a critical concentration, gelation occurs. For the conditions that we have used, gelation occurred at very low initial apo-alpha-lactalbumin concentrations of 34% (w/v), indicating a very dilute cross-linked protein network, with a low average number of cross-links per protein. It is found that reactive protein monomers are first rapidly (1-2 h) incorporated into small covalent clusters. This is followed by a much slower phase (up to about 12 h) in which the small clusters are coupled together to form much larger covalent protein

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

    PubMed

    Savadkoohi, Sobhan; Kasapis, Stefan

    2016-07-01

    High pressure technology is the outcome of consumer demand for better quality control of processed foods. There is great potential to apply HPP to condensed systems of globular proteins for the generation of industry-relevant biomaterials with advanced techno- and biofunctionality. To this end, research demonstrates that application of high hydrostatic pressure generates a coherent structure and preserves the native conformation in condensed globular proteins, which is an entirely unexpected but interesting outcome on both scientific and technological grounds. In microbiological challenge tests, high pressure at conventional commercial conditions, demonstrated to effectively reduce the concentration of typical Gram negative or Gram positive foodborne pathogens, and proteolytic enzymes in high-solid protein samples. This may have industrial significance in relation to the formulation and stabilisation of "functional food" products as well as in protein ingredients and concentrates by replacing spray dried powders with condensed HPP-treated pastes that maintain structure and bioactivity. Fundamental concepts and structural functionality of condensed matrices of globular proteins are the primary interest in this mini-review, which may lead to opportunities for industrial exploitation, but earlier work on low-solid systems is also summarised presently to put recent developments in context of this rapidly growing field. PMID:27060534

  18. 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

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

    PubMed

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

    2016-01-01

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

  20. The small angle x-ray scattering of globular proteins in solution during heat denaturation

    NASA Astrophysics Data System (ADS)

    Banuelos, Jose; Urquidi, Jacob

    2008-10-01

    The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as a change in temperature, pressure, and the introduction of ions into the aqueous environment of a protein can give rise to the folding/unfolding of a protein. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for five globular proteins. Trends in the observed intermediate structures of these globular proteins, along with correlations with data on protein thermodynamics may help elucidate shared characteristics between all proteins in the folding/unfolding process. Experimental design considerations will be discussed and preliminary results for some of these systems will be presented.

  1. Nanostructure and new properties of hydrolyzed food globular proteins

    NASA Astrophysics Data System (ADS)

    Rogov, I. A.; Danilchuk, T. N.; Shushkevich, J. A.; Semenov, G. V.; Ovchinnikova, O. E.

    2011-04-01

    In the present work we obtained a hydrolysates of food proteins by enzyme hydrolysis, researched the comparative structural and the molecular - mass characteristics of proteins, and compared of hydrolysates particles structural characteristics on nanoscale with their biological properties.

  2. 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.

  3. 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

  4. 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

  5. Finite Size Effects on Thermal Denaturation of Globular Proteins

    NASA Astrophysics Data System (ADS)

    Li, Mai Suan; Klimov, Dmitri K.; Thirumalai, D.

    2004-12-01

    Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Ωc, scales as Nζ, where N is the number of amino acids. Surprisingly, we find that ζ is universal with ζ=1+γ, where the exponent γ characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires TF≈Tθ, where Tθ and TF are the collapse and folding transition temperatures, respectively.

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

    PubMed

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

    2015-06-01

    The interactions between water-soluble semiconductor quantum dots [hydrophilic 3-mercaptopropionic acid (MPA)-coated CdSe] and three globular plasma proteins, namely, bovine serum albumin (BSA), β-lactoglobulin (β-Lg) and human serum albumin (HSA), are investigated. Acidic residues of protein molecules form electrostatic interactions with these quantum dots (QDs). To determine the stoichiometry of proteins bound to QDs, we used dynamic light scattering (DLS) and zeta potential techniques. Fluorescence resonance energy transfer (FRET) experiments revealed energy transfer from tryptophan residues in the proteins to the QD particles. Quenching of the intrinsic fluorescence of protein molecules was noticed during this binding process (hierarchy HSA<β-Lg protein molecules). Upon binding with QD particles, the protein molecules underwent substantial conformational changes at the secondary-structure level (50 % helicity lost), due to loss in hydration. PMID:25767054

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

    DOE PAGESBeta

    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

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

    PubMed

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

    2015-06-01

    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

  9. Acceleration of hybrid MPI parallel NBODY6++ for large N-body globular cluster simulations

    NASA Astrophysics Data System (ADS)

    Wang, Long; Spurzem, Rainer; Aarseth, Sverre; Nitadori, Keigo; Berczik, Peter; Kouwenhoven, M. B. N.; Naab, Thorsten

    2016-02-01

    Previous research on globular clusters (GCs) dynamics is mostly based on semi-analytic, Fokker-Planck, Monte-Carlo methods and on direct N-body (NB) simulations. These works have great advantages but also limits since GCs are massive and compact and close encounters and binaries play very important roles in their dynamics. The former three methods make approximations and assumptions, while expensive computing time and number of stars limit the latter method. The current largest direct NB simulation has ~ 500k stars (Heggie 2014). Here, we accelerate the direct NB code NBODY6++ (which extends NBODY6 to supercomputers by using MPI) with new parallel computing technologies (GPU, OpenMP + SSE/AVX). Our aim is to handle large N (up to 106) direct NB simulations to obtain better understanding of the dynamical evolution of GCs.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Tiana, G.; Sutto, L.

    2011-12-01

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

  12. 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

  13. 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.

  14. 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.

  15. Contribution of Charged Groups to the Enthalpic Stabilization of the Folded States of Globular Proteins

    PubMed Central

    Dadarlat, Voichita M.; Post, Carol Beth

    2016-01-01

    In this paper we use the results from all atom MD simulations of proteins and peptides to assess individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the “unfolded state”) and charged amino acids in globular proteins (the “folded state”). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO−) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while NH3+ groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously. PMID:18303881

  16. 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

  17. 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

  18. 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.

  19. Light-fuelled transport of large dendrimers and proteins.

    PubMed

    Koskela, Jenni E; Liljeström, Ville; Lim, Jongdoo; Simanek, Eric E; Ras, Robin H A; Priimagi, Arri; Kostiainen, Mauri A

    2014-05-14

    This work presents a facile water-based supramolecular approach for light-induced surface patterning. The method is based upon azobenzene-functionalized high-molecular weight triazine dendrimers up to generation 9, demonstrating that even very large globular supramolecular complexes can be made to move in response to light. We also demonstrate light-fuelled macroscopic movements in native biomolecules, showing that complexes of apoferritin protein and azobenzene can effectively form light-induced surface patterns. Fundamentally, the results establish that thin films comprising both flexible and rigid globular particles of large diameter can be moved with light, whereas the presented material concepts offer new possibilities for the yet marginally explored biological applications of azobenzene surface patterning. PMID:24785836

  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 Central

    2015-01-01

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

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

    SciTech Connect

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

    2013-12-05

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

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

    SciTech Connect

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

    2014-06-01

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

  6. Salt-induced gelation of globular protein aggregates: structure and kinetics.

    PubMed

    Ako, Komla; Nicolai, Taco; Durand, Dominique

    2010-04-12

    Aggregates of the globular protein beta-lactoglobulin were formed by heating solutions of native proteins at pH 7, after which gels were formed by the addition of salt. The second step does not necessitate elevated temperatures and is therefore often called cold gelation. The structure of the gels was studied during their formation using light scattering and turbidity. Complementary confocal laser scanning microscopy measurements were done. We compared the structure with that of gels formed by heating native beta-lactoglobulin under the same conditions. Whereas in the latter case, microphase separation occurs above 0.2 M NaCl, no microphase separation was observed during cold gelation up to at least 1 M NaCl. The dependence of the kinetics and the final gel structure on the protein concentration, the temperature, the salt concentration, and the aggregate size was quantified. A few measurements on gels formed by adding CaCl(2) confirmed the higher efficiency of this bivalent cation but revealed no qualitative differences with gels formed by adding NaCl. PMID:20297835

  7. Molecular description of the formation and structure of plasticized globular protein films.

    PubMed

    Lefèvre, Thierry; Subirade, Muriel; Pézolet, Michel

    2005-01-01

    To optimize the properties of plasticized globular proteins films, a clear comprehension of the structure and molecular events occurring during film formation is required. In this work, the structural organization of beta-lactoglobulin (beta-lg) films plasticized with diethyelene glycol are investigated for the first time during the entire film formation process by attenuated total reflectance and transmission infrared spectroscopy. The films are made by a common two-step procedure consisting of a first heat treatment (80 degrees C/30 min) followed by the casting of the film-forming solution for dehydration. Heating at 80 degrees C leads to the self-aggregation of the proteins with a conversion of regular secondary structures into antiparallel beta-sheets. The kinetics of the conformational conversion shows that approximately 10% of the amino acids are involved in beta-sheets after the first step. Dehydration induces a further aggregation, with approximately 46% of the amino acids involved in beta-sheets in the final film. Water evaporation results in the association of the aggregates formed during the heating step. The presence of the plasticizer during water removal is essential as it allows specific conformational rearrangements into extended beta-sheets and ordering of the polypeptide chains. This work underlines that the assembly of building blocks is common in beta-lg networks and it emphasizes the widespread occurrence of beta-structures in synthetic and natural protein networks. PMID:16283748

  8. 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

  9. Molecular determinants of expansivity of native globular proteins: a pressure perturbation calorimetry study.

    PubMed

    Vasilchuk, Daniel; Pandharipande, Pranav P; Suladze, Saba; Sanchez-Ruiz, Jose M; Makhatadze, George I

    2014-06-12

    There is a growing interest in understanding how hydrostatic pressure (P) impacts the thermodynamic stability (ΔG) of globular proteins. The pressure dependence of stability is defined by the change in volume upon denaturation, ΔV = (∂ΔG/∂P)T. The temperature dependence of change in volume upon denaturation itself is defined by the changes in thermal expansivity (ΔE), ΔE = (∂ΔV/∂T)P. The pressure perturbation calorimetry (PPC) allows direct experimental measurement of the thermal expansion coefficient, α = E/V, of a protein in the native, αN(T), and unfolded, αU(T), states as a function of temperature. We have shown previously that αU(T) is a nonlinear function of temperature but can be predicted well from the amino acid sequence using α(T) values for individual amino acids (J. Phys. Chem. B 2010, 114, 16166-16170). In this work, we report PPC results on a diverse set of nine proteins and discuss molecular factors that can potentially influence the thermal expansion coefficient, αN(T), and the thermal expansivity, EN(T), of proteins in the native state. Direct experimental measurements by PPC show that αN(T) and EN(T) functions vary significantly for different proteins. Using comparative analysis and site-directed mutagenesis, we have eliminated the role of various structural or thermodynamic properties of these proteins such as the number of amino acid residues, secondary structure content, packing density, electrostriction, dynamics, or thermostability. We have also shown that αN(T) and EN,sp(T) functions for a given protein are rather insensitive to the small changes in the amino acid sequence, suggesting that αN(T) and EN(T) functions might be defined by a topology of a given protein fold. This conclusion is supported by the similarity of αN(T) and EN(T) functions for six resurrected ancestral thioredoxins that vary in sequence but have very similar tertiary structure. PMID:24849138

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

    PubMed

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

    2016-07-15

    This is a second part of the three-part article from a series of reviews on the abundance and roles of intrinsic disorder in milk proteins. We continue to describe α-lactalbumin, a small globular Ca2+-binding protein, which besides being one of the two components of lactose synthase that catalyzes the final step of the lactose biosynthesis in the lactating mammary gland, possesses a multitude of other functions. In fact, recent studies indicated that some partially folded forms of this protein possess noticeable bactericidal activity and other forms might be related to induction of the apoptosis of tumor cells. In its anti-tumorigenic function, oligomeric α-lactalbumin serves as a founding member of a new family of anticancer drugs termed liprotides (for lipids and partially denatured proteins), where an oligomeric molten globular protein acts as an "oil container" or cargo for the delivery of oleic acid to the cell membranes. PMID:26916155

  11. 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

  12. Intermediate states of globular proteins during temperature-induced folding and unfolding studied using small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Banuelos, Jose; Urquidi, Jacob

    2009-03-01

    The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as concentration, degree of crowding from other entities, and solvent medium affect how a protein folds. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for a series of globular proteins. The temporal stability of these ensembles is also under investigation. Trends in the scattering profiles, along with correlations with protein thermodynamics, may help elucidate shared characteristics between all proteins in their folding behavior.

  13. 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

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

    PubMed

    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

  15. 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.

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

    PubMed

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

    2003-11-21

    A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature. PMID:14631033

  17. 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

  18. 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. PMID:26660714

  19. 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.

  20. 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.

  1. The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.

    PubMed

    Takashima, S

    2001-04-01

    The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments. PMID:11180053

  2. 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; Pereira de Araújo, Antônio F

    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. Proteins 2016; 84:515-531. © 2016 Wiley Periodicals, Inc. PMID:26815167

  3. 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.

  4. 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.

  5. 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.

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

    SciTech Connect

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

    2013-06-10

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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.

    PubMed

    Ryabov, Yaroslav E; Geraghty, Charles; Varshney, Amitabh; Fushman, David

    2006-12-01

    We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138-146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins. PMID:17132010

  12. Most of the structural elements of the globular domain of murine prion protein form fibrils with predominant beta-sheet structure.

    PubMed

    Jamin, Nadège; Coïc, Yves-Marie; Landon, Céline; Ovtracht, Ludmila; Baleux, Françoise; Neumann, Jean-Michel; Sanson, Alain

    2002-10-01

    The conversion of the cellular prion protein into the beta-sheet-rich scrapie prion protein is thought to be the key step in the pathogenesis of prion diseases. To gain insight into this structural conversion, we analyzed the intrinsic structural propensity of the amino acid sequence of the murine prion C-terminal domain. For that purpose, this globular domain was dissected into its secondary structural elements and the structural propensity of the protein fragments was determined. Our results show that all these fragments, excepted that strictly encompassing helix 1, have a very high propensity to form structured aggregates with a dominant content of beta-sheet structures. PMID:12372610

  13. 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

  14. Heat-induced gelation of globular proteins: part 3. Molecular studies on low pH beta-lactoglobulin gels.

    PubMed

    Kavanagh, G M; Clark, A H; Ross-Murphy, S B

    2000-10-10

    Heat-set gels and aggregates from beta-lactoglobulin (beta-Lg), one of the major globular proteins from milk, have been studied on a molecular distance scale using negative-staining transmission electron microscopy (TEM), wide-angle X-ray diffraction (WAXD), and Fourier transform infrared spectroscopy (FTIR). The microscopy showed long linear aggregates forming in solutions at pH 2 (and sometimes 2.5) after prolonged heating. While there appeared to be no differences in aggregates formed under these conditions in H(2)O as compared with D(2)O, at all other pH and pD values, and in the presence of added salt, much shorter linear aggregates were formed. These became slightly more extended the further the pH was removed from pI. Wide-angle X-ray diffraction (WAXD) showed a diffuse beta-sheet halo at 2θ=19 degrees in patterns for both dried native and aggregated protein (irrespective of pH) with only a small change (sharpening) of this feature on heat treatment. Solution FTIR spectra, measured at pD=2, 2.5, 3, and 7, during heating, indicated shoulder development at 1612 cm(-1) in the carbonyl-stretching Amide I region diagnostic of a modest increase in intermolecular beta-sheet. In terms of the shoulder size, no distinctions could be made between acid and neutral aggregate structures. At all pHs, beta-lactoglobulin showed only limited secondary and tertiary structural changes in aggregation, in contrast to previous studies of insulin aggregation, where highly ordered crystalline fibrils were indicated. The current work has implications both in structural studies of food biopolymers and in ongoing studies of pathological protein self-assembly in disease states, such as spongiform encephalopathies. PMID:11033176

  15. ATP-dependent Proteases Differ Substantially in Their Ability to Unfold Globular Proteins*

    PubMed Central

    Koodathingal, Prakash; Jaffe, Neil E.; Kraut, Daniel A.; Prakash, Sumit; Fishbain, Susan; Herman, Christophe; Matouschek, Andreas

    2009-01-01

    ATP-dependent proteases control the concentrations of hundreds of regulatory proteins and remove damaged or misfolded proteins from cells. They select their substrates primarily by recognizing sequence motifs or covalent modifications. Once a substrate is bound to the protease, it has to be unfolded and translocated into the proteolytic chamber to be degraded. Some proteases appear to be promiscuous, degrading substrates with poorly defined targeting signals, which suggests that selectivity may be controlled at additional levels. Here we compare the abilities of representatives from all classes of ATP-dependent proteases to unfold a model substrate protein and find that the unfolding abilities range over more than 2 orders of magnitude. We propose that these differences in unfolding abilities contribute to the fates of substrate proteins and may act as a further layer of selectivity during protein destruction. PMID:19383601

  16. 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.

  17. Towards an intelligent system for the automatic assignment of domains in globular proteins.

    PubMed

    Sternberg, M J; Hegyi, H; Islam, S A; Luo, J; Russell, R B

    1995-01-01

    The automatic identification of protein domains from coordinates is the first step in the classification of protein folds and hence is required for databases to guide structure prediction. Most algorithms encode a single concept based and sometimes do not yield assignments that are consistent with the generally accepted perception. Our development of an automatic approach to identify reliably domains from protein coordinates is described. The algorithm is benchmarked against a manual identification of the domains in 284 representative protein chains. The first step is the domain assignment by distance (DAD) algorithm that considers the density of inter-residue contacts represented in a contact matrix. The algorithm yields 85% agreement with the manual assignment. The paper then considers how the reliability of these assignments could be evaluated. Finally the use of structural comparisons using the STAMP algorithm to validate domain assignment is reported on a test case. PMID:7584461

  18. Investigation of deprotonation reactions on globular and denatured proteins at atmospheric pressure by ESSI-MS.

    PubMed

    Touboul, David; Jecklin, Matthias Conradin; Zenobi, Renato

    2008-04-01

    Deprotonation reactions of multiply charged protein ions have been studied by introducing volatile reference bases at atmospheric pressure between an electrosonic spray ionization (ESSI) source and the inlet of a mass spectrometer. Apparent gas-phase basicities (GB(app)) of different charge states of protein ions were determined by a bracketing approach. The results obtained depend on the conformation of the protein ions in the gas phase, which is linked to the type of buffer used (denaturing or nondenaturing). In nondenaturing buffer, the GB(app) values are consistent with values predicted by the group of Kebarle using an electrostatic model (J. Mass Spectrom.2002, 38, 618) based on the crystal structures, but taking into account salt bridges between ionized basic and acidic sites on the protein surface. A new basicity order for the most basic sites was therefore obtained. An excellent agreement with the charge residue model (CRM) is obtained when comparing the observed and calculated maximum charge state. Decharging of the proteins in the electrosonic spray process could be also useful in the study on noncovalent complexes, by decreasing repulsive electrostatic interactions. A unified mechanism of the ESSI process is proposed. PMID:18276154

  19. 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.

  20. 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

  1. Extended Law of Corresponding States Applied to Solvent Isotope Effect on a Globular Protein.

    PubMed

    Bucciarelli, Saskia; Mahmoudi, Najet; Casal-Dujat, Lucía; Jéhannin, Marie; Jud, Corinne; Stradner, Anna

    2016-05-01

    Investigating proteins with techniques such as NMR or neutron scattering frequently requires the partial or complete substitution of D2O for H2O as a solvent, often tacitly assuming that such a solvent substitution does not significantly alter the properties of the protein. Here, we report a systematic investigation of the solvent isotope effect on the phase diagram of the lens protein γB-crystallin in aqueous solution as a model system exhibiting liquid-liquid phase separation. We demonstrate that the observed strong variation of the critical temperature Tc can be described by the extended law of corresponding states for all H2O/D2O ratios, where scaling of the temperature by Tc or the reduced second virial coefficient accurately reproduces the binodal, spinodal, and osmotic compressibility. These findings highlight the impact of H2O/D2O substitution on γB-crystallin properties and warrant further investigations into the universality of this phenomenon and its underlying mechanisms. PMID:27077243

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

    NASA Astrophysics Data System (ADS)

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

    2000-12-01

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

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

    DOE PAGESBeta

    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

  4. 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. PMID:26266736

  5. Molecular crowding enhances native state stability and refolding rates of globular proteins

    NASA Astrophysics Data System (ADS)

    Cheung, Margaret S.; Klimov, Dmitri; Thirumalai, D.

    2005-03-01

    The presence of macromolecules in cells geometrically restricts the available space for poplypeptide chains. To study the effects of macromolecular crowding on folding thermodynamics and kinetics, we used an off-lattice model of the all--sheet WW domain in the presence of large spherical particles whose interaction with the polypeptide chain is purely repulsive. At all volume fractions, c, of the crowding agents the stability of the native state is enhanced. Remarkably, the refolding rates, which are larger than the value at c = 0, increase nonmonotonically as c increases, reaching a maximum at . At high values of c, the depletion-induced intramolecular attraction produces compact structures with considerable structure in the denatured state. Changes in native state stability and folding kinetics at c can be quantitatively mapped onto confinement in a volume-fraction-dependent spherical pore with radius Rs ≈ (4π/3ϕc)1/3 Rc (Rc is the radius of the crowding particles) as long as ϕc is comparable with that in a spherical pore. In both situations, rate enhancement is due to destabilization of the denatured states with respect to ϕc = 0.

  6. 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 Central

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

    2014-01-01

    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. PMID:24356966

  7. Large-scale extraction of proteins.

    PubMed

    Cunha, Teresa; Aires-Barros, Raquel

    2002-01-01

    The production of foreign proteins using selected host with the necessary posttranslational modifications is one of the key successes in modern biotechnology. This methodology allows the industrial production of proteins that otherwise are produced in small quantities. However, the separation and purification of these proteins from the fermentation media constitutes a major bottleneck for the widespread commercialization of recombinant proteins. The major production costs (50-90%) for typical biological product resides in the purification strategy. There is a need for efficient, effective, and economic large-scale bioseparation techniques, to achieve high purity and high recovery, while maintaining the biological activity of the molecule. Aqueous two-phase systems (ATPS) allow process integration as simultaneously separation and concentration of the target protein is achieved, with posterior removal and recycle of the polymer. The ease of scale-up combined with the high partition coefficients obtained allow its potential application in large-scale downstream processing of proteins produced by fermentation. The equipment and the methodology for aqueous two-phase extraction of proteins on a large scale using mixer-settlerand column contractors are described. The operation of the columns, either stagewise or differential, are summarized. A brief description of the methods used to account for mass transfer coefficients, hydrodynamics parameters of hold-up, drop size, and velocity, back mixing in the phases, and flooding performance, required for column design, is also provided. PMID:11876297

  8. 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

  9. 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

  10. Modified interactions among globular proteins below isoelectric point in the presence of mono-, di- and tri-valent ions: A small angle neutron scattering study

    NASA Astrophysics Data System (ADS)

    Das, Kaushik; Kundu, Sarathi; Mehan, Sumit; Aswal, V. K.

    2016-02-01

    Both short range attraction and long range electrostatic repulsion exist among globular protein Bovine Serum Albumin in solution below its isoelectric point (pI ≈ 4.8). At pD ≈ 4.0, below pI, protein has a net positive surface charge although local charge inhomogeneity presents. Small angle neutron scattering study reveals that in the presence of both mono-(Na+) and di-(Ni2+) valent ions attractive interaction increases and repulsive interaction decreases with the increase of salt concentration. However, for tri-valent (Fe3+) ions, both attractive and repulsive interaction increases with increasing salt concentration but the relative strength of repulsion is more than the attraction.

  11. Experimental evidence of distance-dependent diffusion coefficients of a globular protein observed in polymer aqueous solution forming a network structure on nanometer scale

    NASA Astrophysics Data System (ADS)

    Masuda, Akiko; Ushida, Kiminori; Nishimura, Goro; Kinjo, Masataka; Tamura, Mamoru; Koshino, Hiroyuki; Yamashita, Koichi; Kluge, Thomas

    2004-12-01

    The distance dependence of the diffusion coefficient (DDDC) of a globular protein (cytchrome c) in aqueous hyaluronan (HA) solution, which is a model system for extracellular matrices (ECMs), was measured by a combination of three kinds of spectroscopic measurements of diffusion coefficients, the time and space samplings of which are different. The results of the three methods are plotted against the diffusion distance derived from the consideration of each experimental condition. Due to the characteristic morphology of HA with an effective mesh structure, the proteins showed two extreme diffusion modes: (1) short (<10 nm) diffusion with rare contact with polymer chains; (2) long (>100 nm) diffusion significantly disrupted by polymer chains showing an ≈30% reduction in diffusion coefficient. The transition from the short diffusion to the long one occurs in a very narrow range (10-100 nm) of diffusion distance and this unique character of HA realizing anomalous diffusion should provide suitable environments for various bioactivities when involved in ECM.

  12. Thermodynamics, kinetics, and salt-dependence of folding of YopM, a large leucine-rich repeat protein

    PubMed Central

    Kloss, Ellen; Barrick, Doug

    2011-01-01

    Small globular proteins have many contacts between residues that are distant in primary sequence. These contacts create a complex network between sequence-distant segments of secondary structure, which may be expected to promote the cooperative folding of globular proteins. Although repeat proteins, which are made up of tandem modular units, lack sequence-distant contacts, several of considerable length have been shown to undergo cooperative two-state folding. To explore the limits of cooperativity in repeat proteins, we have studied the unfolding of YopM, a leucine-rich repeat (LRR) protein of over 400 residues. Despite its large size and modular architecture (15 repeats), YopM equilibrium unfolding is highly cooperative, and shows a very strong dependence on urea concentration. In contrast, kinetic studies of YopM folding indicate a mechanism that includes one or more transient intermediates. The urea dependence of the folding and unfolding rates suggests a relatively small transition state ensemble. As with the urea dependence, we have found an extreme dependence of the free energy of unfolding on salt concentration. This salt dependence likely results from general screening of a large number of unfavorable columbic interactions in the folded state, rather than from specific cation binding. PMID:18793647

  13. 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.

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

    PubMed Central

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

    2015-01-01

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

  15. 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.

  16. 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.

  17. CVs and millisecond pulsar progenitors in globular clusters

    NASA Technical Reports Server (NTRS)

    Grindlay, J. E.; Cool, A. M.; Bailyn, C. D.

    1991-01-01

    The recent discovery of a large population of millisecond pulsars in globular clusters, together with earlier studies of both low luminosity X-ray sources and LMXBs in globulars, suggest there should be significant numbers of CVs in globulars. Although they have been searched for without success in selected cluster X-ray source fields, systematic surveys are lacking and would constrain binary production and both stellar and dynamical evolution in globular clusters. We describe the beginnings of such a search, using narrow band H-alpha imaging, and the sensitivities it might achieve.

  18. C1q-TNF-related protein-9, a novel cardioprotetcive cardiokine, requires proteolytic cleavage to generate a biologically active globular domain isoform.

    PubMed

    Yuan, Yuexing; Lau, Wayne Bond; Su, Hui; Sun, Yang; Yi, Wei; Du, Yunhui; Christopher, Theodore; Lopez, Bernard; Wang, Yajing; Ma, Xin-Liang

    2015-05-15

    Prevalence and severity of postmyocardial infarction heart failure continually escalate in type 2 diabetes via incompletely understood mechanisms. The discovery of the cardiac secretomes, collectively known as "cardiokines", has significantly enhanced appreciation of the local microenvironment's influence on disease development. Recent studies demonstrated that C1q-TNF-related protein-9 (CTRP9), a newly discovered adiponectin (APN) paralog, is highly expressed in the heart. However, its relationship with APN (concerning diabetic cardiovascular injury in particular) remains unknown. Plasma CTRP9 levels are elevated in APN knockout and reduced in diabetic mice. In contrast to APN, which circulates as full-length multimers, CTRP9 circulates in the plasma primarily in the globular domain isoform (gCTRP9). Recombinant full-length CTRP9 (fCTRP9) was cleaved when incubated with cardiac tissue extracts, generating gCTRP9, a process inhibited by protease inhibitor cocktail. gCTRP9 rapidly activates cardiac survival kinases, including AMPK, Akt, and endothelial NOS. However, fCTRP9-mediated kinase activation is much less potent and significantly delayed. Kinase activation by fCTRP9, but not gCTRP9, is inhibited by protease inhibitor cocktail. These results demonstrate for the first time that the novel cardiokine CTRP9 undergoes proteolytic cleavage to generate gCTRP9, the dominant circulatory and actively cardioprotective isoform. Enhancing cardiac CTRP9 production and/or its proteolytic posttranslational modification are of therapeutic potential, attenuating diabetic cardiac injury. PMID:25783894

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

    PubMed Central

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

    1994-01-01

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

  20. 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

  1. Globular Cluster Abundances from High-resolution, Integrated-light Spectroscopy. IV. The Large Magellanic Cloud: α, Fe-peak, Light, and Heavy Elements

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    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 ~ 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 χ2-minimization spectral synthesis technique to facilitate measurement of weak (~15 mÅ) spectral lines and abundances in low signal-to-noise ratio data (S/N ~ 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 [α/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 results can be used to constrain both

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Chatterjee, Prathit; Bagchi, Sayan; Sengupta, Neelanjana

    2014-11-01

    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 (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc 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 Tc in comparison to Ts. 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 Tc. 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 Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. 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.

  7. 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

  8. Massive star archeology in globular clusters

    NASA Astrophysics Data System (ADS)

    Chantereau, W.; Charbonnel, C.; Meynet, G.

    2015-01-01

    Globular clusters are among the oldest structures in the Universe and they host today low-mass stars and no gas. However, there has been a time when they formed as gaseous objects hosting a large number of short-lived, massive stars. Many details on this early epoch have been depicted recently through unprecedented dissection of low-mass globular cluster stars via spectroscopy and photometry. In particular, multiple populations have been identified, which bear the nucleosynthetic fingerprints of the massive hot stars disappeared a long time ago. Here we discuss how massive star archeology can be done through the lense of these multiple populations.

  9. 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.

  10. 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

  11. Luminosity Functions for Globular Clusters

    NASA Astrophysics Data System (ADS)

    Silvestri, Fabio; Ventura, Paolo; D'Antona, Francesca; Mazzitelli, Italo

    1998-12-01

    We present theoretical mass-luminosity relations and luminosity functions (LFs) for globular cluster stars, from luminosities above the horizontal branch down to the minimum luminosity of hydrogen-burning stars. The LFs are available for metal mass fraction Z from Z = 10-4 to Z = 4 × 10-3, in the Johnson V band and in the Bessell-Cousins I band, and are based on tracks especially computed for this program, with the input physics of the models developed recently by D'Antona et al., Mazzitelli et al., and D'Antona & Mazzitelli. Two typical comparisons with observations are presented and discussed: (1) comparisons and statistical analysis with the LFs of the lower giant branch, turnoff region, and upper main sequence of several globular clusters from low to high metallicity, (2) derivation of the initial mass function (IMF) for the stars below the turnoff for several globular clusters for which Hubble Space Telescope data are available. In the first analysis we find that, for relatively large metallicities (Z >= 10-3) a good fit between theoretical and observed LFs can be found, although a simple χ2 statistical analysis shows that it is not possible to derive a strongly preferred age (or, equivalently, distance modulus) from the LF comparison. The fit with lower metallicity [Z ~ (1-2) × 10-4] LFs is less good but statistically acceptable. The main result is that the difference between observed and theoretical LFs of low-metallicity clusters reported by VandenBerg, Bolte, & Stetson appears to be much reduced in present models, and we give the possible reason why this happens and its consequences for the important parameter of the helium core mass at the flash. In the second application, we explore the effect of varying age and distance modulus on the mass function derived for a globular cluster. Distance moduli corresponding to the ``long'' distance scale (and relatively low ages) seem to be preferred based on these comparisons. The resulting index of the IMF is

  12. Proteomics beyond large-scale protein expression analysis.

    PubMed

    Boersema, Paul J; Kahraman, Abdullah; Picotti, Paola

    2015-08-01

    Proteomics is commonly referred to as the application of high-throughput approaches to protein expression analysis. Typical results of proteomics studies are inventories of the protein content of a sample or lists of differentially expressed proteins across multiple conditions. Recently, however, an explosion of novel proteomics workflows has significantly expanded proteomics beyond the analysis of protein expression. Targeted proteomics methods, for example, enable the analysis of the fine dynamics of protein systems, such as a specific pathway or a network of interacting proteins, and the determination of protein complex stoichiometries. Structural proteomics tools allow extraction of restraints for structural modeling and identification of structurally altered proteins on a proteome-wide scale. Other variations of the proteomic workflow can be applied to the large-scale analysis of protein activity, location, degradation and turnover. These exciting developments provide new tools for multi-level 'omics' analysis and for the modeling of biological networks in the context of systems biology studies. PMID:25636126

  13. 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.

  14. 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.

  15. 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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. PMID:23353650

  18. 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

  19. 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

  20. Synthesis of globular precursors.

    PubMed

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

    2015-09-01

    o-Carborane (C2 B10 H12 ) was adapted to perform as the core of globular macromolecules, dendrons or dendrimers. To meet this objective, precisely defined substitution patterns of terminal olefin groups on the carborane framework were subjected to Heck cross-coupling reactions or hydroboration leading to hydroxyl terminated arms. These led to new terminal groups (chloro, bromo, and tosyl leaving groups, organic acid, and azide) that permitted ester production, click chemistry, and oxonium ring opening to be performed as examples of reactions that demonstrate the wide possibilities of the globular icosahedral carboranes to produce new dendritic or dendrimer-like structures. Polyanionic species were obtained in high yield through the ring-opening reaction of cyclic oxonium compound [3,3'-Co(8-C4 H8 O2 -1,2-C2 B9 H10 )(1',2'-C2 B9 H11 )] by using terminal hydroxyl groups as nucleophiles. These new polyanionic compounds that contain multiple metallacarborane clusters at their periphery may prove useful as new classes of compounds for boron neutron capture therapy with enhanced water solubility and as cores to make a new class of high-boron globular macromolecules. PMID:26228947

  1. Crystal structures of fusion proteins with large-affinity tags.

    PubMed

    Smyth, Douglas R; Mrozkiewicz, Marek K; McGrath, William J; Listwan, Pawel; Kobe, Bostjan

    2003-07-01

    The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. PMID:12824478

  2. Globular Cluster Colors Versus Population Synthesis Models

    NASA Astrophysics Data System (ADS)

    Barmby, Pauline; Jalilian, F. F.

    2011-05-01

    Although the stellar populations of globular clusters are not as simple as we used to believe, they are still the simplest populations available in the nearby universe. As such, they are extremely useful for testing stellar population synthesis models. Using recent mass estimates for Local Group globular clusters, we have compiled a sample of clusters with masses large enough that stochastic effects on integrated photometry should be minimal. We have measured integrated colors in the Spitzer/IRAC bands for as many of these as possible, paying careful attention to systematics in order to get the most accurate colors. We present a comparison of the results with the predictions of the latest generation of population synthesis models, including GALEV and FSPS. Support for this work was provided by a Discovery Grant and an Undergraduate Summer Research Award from NSERC and by an Ontario Early Researcher Award.

  3. 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.

  4. MODELING THE METALLICITY DISTRIBUTION OF GLOBULAR CLUSTERS

    SciTech Connect

    Muratov, Alexander L.; Gnedin, Oleg Y. E-mail: ognedin@umich.ed

    2010-08-01

    Observed metallicities of globular clusters reflect physical conditions in the interstellar medium of their high-redshift host galaxies. Globular cluster systems in most large galaxies display bimodal color and metallicity distributions, which are often interpreted as indicating two distinct modes of cluster formation. The metal-rich and metal-poor clusters have systematically different locations and kinematics in their host galaxies. However, the red and blue clusters have similar internal properties, such as their masses, sizes, and ages. It is therefore interesting to explore whether both metal-rich and metal-poor clusters could form by a common mechanism and still be consistent with the bimodal distribution. We present such a model, which prescribes the formation of globular clusters semi-analytically using galaxy assembly history from cosmological simulations coupled with observed scaling relations for the amount and metallicity of cold gas available for star formation. We assume that massive star clusters form only during mergers of massive gas-rich galaxies and tune the model parameters to reproduce the observed distribution in the Galaxy. A wide, but not the entire, range of model realizations produces metallicity distributions consistent with the data. We find that early mergers of smaller hosts create exclusively blue clusters, whereas subsequent mergers of more massive galaxies create both red and blue clusters. Thus, bimodality arises naturally as the result of a small number of late massive merger events. This conclusion is not significantly affected by the large uncertainties in our knowledge of the stellar mass and cold gas mass in high-redshift galaxies. The fraction of galactic stellar mass locked in globular clusters declines from over 10% at z > 3 to 0.1% at present.

  5. Photoswitchable red fluorescent protein with a large Stokes shift

    PubMed Central

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

    2014-01-01

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

  6. 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)

  7. Method for Rapid Protein Identification in a Large Database

    PubMed Central

    Zhang, Wenli; Zhao, Xiaofang

    2013-01-01

    Protein identification is an integral part of proteomics research. The available tools to identify proteins in tandem mass spectrometry experiments are not optimized to face current challenges in terms of identification scale and speed owing to the exponential growth of the protein database and the accelerated generation of mass spectrometry data, as well as the demand for nonspecific digestion and post-modifications in complex-sample identification. As a result, a rapid method is required to mitigate such complexity and computation challenges. This paper thus aims to present an open method to prevent enzyme and modification specificity on a large database. This paper designed and developed a distributed program to facilitate application to computer resources. With this optimization, nearly linear speedup and real-time support are achieved on a large database with nonspecific digestion, thus enabling testing with two classical large protein databases in a 20-blade cluster. This work aids in the discovery of more significant biological results, such as modification sites, and enables the identification of more complex samples, such as metaproteomics samples. PMID:24000323

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

    PubMed Central

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

    2011-01-01

    Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences. PMID:22046139

  9. 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. PMID:22046139

  10. Characterization of the murine gene of gC1qBP, a novel cell protein that binds the globular heads of C1q, vitronectin, high molecular weight kininogen and factor XII.

    PubMed

    Lim, B L; White, R A; Hummel, G S; Schwaeble, W; Lynch, N J; Peerschke, E I; Reid, K B; Ghebrehiwet, B

    1998-03-16

    gC1qBP is a novel cell protein which was found to interact with the globular heads of C1q, high mol. wt kininogen, factor XII and the heparin-binding, multimeric form of vitronectin. The protein sequence shows no homology to any protein family. This paper describes the genomic organization of mouse gC1qBP and the characterization of its 5' flanking region. The mouse gene consists of six exons separated by five introns, and its total length is approximately 6kb. Exon 1 encodes the putative signal peptide, a long stretch of 70 amino acid residues, and the first four amino acid residues found in the mature gC1qBP. Exons 2-5 encode four very hydrophilic domains, whereas exon 6 encodes a neutral domain. The amino acid sequence responsible for binding to the heparin-binding, multimeric form of vitronectin is located in exon 2. A 1kb DNA fragment upstream of the first initiation codon was sequenced, which contained four potential TATA boxes, seven CAAT boxes, six SP1 sites and various putative transcription factor-binding elements, indicating that the promoter region is in close proximity to the first exon. The mouseC1qbp gene was mapped to chromosome 11, closely linked to D11Mit4 using genomic DNAs from a (C57BL/6J x Mus spretus)F1 x Mus spretus backcross. PMID:9524273

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

    PubMed Central

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

    2015-01-01

    With the rapid increase in crystal structures of protein-protein complexes deposited in the Protein Data Bank (PDB), more and more crystal contacts have been shown to have similar or even larger interface areas than biological interfaces. However, little attention has been paid to these large crystal packing contacts and their structural principles remain unknown. To address this issue, we used a comparative feature analysis to analyze the geometric and physicochemical properties of large crystal packing contacts by comparing two types of specific protein-protein interactions (PPIs), weak transient complexes and permanent homodimers. Our results show that although large crystal packing contacts have a similar interface area and contact size as permanent homodimers, they tend to be more planar, loosely packed and less hydrophobic than permanent homodimers and cannot form a central core region that is fully buried during interaction. However, the properties of large crystal packing contacts, except for the interface area and contact size, more closely resemble those of weak transient complexes. The large overlap between biological and large crystal packing contacts indicates that interface properties are not efficient indicators for classification of biological interfaces from large crystal packing contacts and finding other specific features urgently needed. PMID:26370141

  12. Analyzing Large Protein Complexes by Structural Mass Spectrometry

    PubMed Central

    Kirshenbaum, Noam; Michaelevski, Izhak; Sharon, Michal

    2010-01-01

    Living cells control and regulate their biological processes through the coordinated action of a large number of proteins that assemble themselves into an array of dynamic, multi-protein complexes1. To gain a mechanistic understanding of the various cellular processes, it is crucial to determine the structure of such protein complexes, and reveal how their structural organization dictates their function. Many aspects of multi-protein complexes are, however, difficult to characterize, due to their heterogeneous nature, asymmetric structure, and dynamics. Therefore, new approaches are required for the study of the tertiary levels of protein organization. One of the emerging structural biology tools for analyzing macromolecular complexes is mass spectrometry (MS)2-5. This method yields information on the complex protein composition, subunit stoichiometry, and structural topology. The power of MS derives from its high sensitivity and, as a consequence, low sample requirement, which enables examination of protein complexes expressed at endogenous levels. Another advantage is the speed of analysis, which allows monitoring of reactions in real time. Moreover, the technique can simultaneously measure the characteristics of separate populations co-existing in a mixture. Here, we describe a detailed protocol for the application of structural MS to the analysis of large protein assemblies. The procedure begins with the preparation of gold-coated capillaries for nanoflow electrospray ionization (nESI). It then continues with sample preparation, emphasizing the buffer conditions which should be compatible with nESI on the one hand, and enable to maintain complexes intact on the other. We then explain, step-by-step, how to optimize the experimental conditions for high mass measurements and acquire MS and tandem MS spectra. Finally, we chart the data processing and analyses that follow. Rather than attempting to characterize every aspect of protein assemblies, this protocol

  13. Mutational effects on stability are largely conserved during protein evolution.

    PubMed

    Ashenberg, Orr; Gong, L Ian; Bloom, Jesse D

    2013-12-24

    Protein stability and folding are the result of cooperative interactions among many residues, yet phylogenetic approaches assume that sites are independent. This discrepancy has engendered concerns about large evolutionary shifts in mutational effects that might confound phylogenetic approaches. Here we experimentally investigate this issue by introducing the same mutations into a set of diverged homologs of the influenza nucleoprotein and measuring the effects on stability. We find that mutational effects on stability are largely conserved across the homologs. We reach qualitatively similar conclusions when we simulate protein evolution with molecular-mechanics force fields. Our results do not mean that proteins evolve without epistasis, which can still arise even when mutational stability effects are conserved. However, our findings indicate that large evolutionary shifts in mutational effects on stability are rare, at least among homologs with similar structures and functions. We suggest that properly describing the clearly observable and highly conserved amino acid preferences at individual sites is likely to be far more important for phylogenetic analyses than accounting for rare shifts in amino acid propensities due to site covariation. PMID:24324165

  14. 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.

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

    PubMed Central

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

    2009-01-01

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

  16. 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.

  17. 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.

  18. PRIONS: PATHOLOGICAL PROTEINS AT THE INTERFACE OF OIL AND WATER.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A prion is an infectious isoform (PrPSc) of a normal cellular protein (PrPC). PrPC is a globular protein composed of approximately 209 amino acids, depending on species. It has three post-translational modifications (PTM): a disulfide linkage, two large sugar antennae, and a glycosyl phosphatidylino...

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

    PubMed

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

    2016-08-01

    Manassantin A is a natural product that has been shown to have anticancer activity in cell-based assays, but has a largely unknown mode-of-action. Described here is the use of two different energetics-based approaches to identify protein targets of manassantin A. Using the stability of proteins from rates of oxidation technique with an isobaric mass tagging strategy (iTRAQ-SPROX) and the pulse proteolysis technique with a stable isotope labeling with amino acids in cell culture strategy (SILAC-PP), over 1000 proteins in a MDA-MB-231 cell lysate grown under hypoxic conditions were assayed for manassantin A interactions (both direct and indirect). A total of 28 protein hits were identified with manassantin A-induced thermodynamic stability changes. Two of the protein hits (filamin A and elongation factor 1α) were identified using both experimental approaches. The remaining 26 hit proteins were only assayed in either the iTRAQ-SPROX or the SILAC-PP experiment. The 28 potential protein targets of manassantin A identified here provide new experimental avenues along which to explore the molecular basis of manassantin A's mode of action. The current work also represents the first application iTRAQ-SPROX and SILAC-PP to the large-scale analysis of protein-ligand binding interactions involving a potential anticancer drug with an unknown mode-of-action. PMID:27322910

  20. 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.

  1. 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.

  2. Chemical Abundance Patterns of Galactic Bulge Globular Clusters

    NASA Astrophysics Data System (ADS)

    Johnson, Christian I.; Rich, R. M.; Kunder, A.; Pilachowski, C. A.

    2014-01-01

    The Galactic bulge globular clusters are interesting but poorly understood stellar systems. The number of bulge globular cluster stars for which detailed chemical abundance information is available is considerably smaller than for halo cluster stars. However, there is growing evidence that many of the bulge globular clusters exhibit interesting characteristics, such as: double horizontal branches, populations separated by more than a factor of two in metallicity, high metallicity clusters with very blue horizontal branches, and large star-to-star variations of heavy element abundances. In order to investigate some of these problems, we have obtained high resolution spectra of several stars in multiple bulge globular clusters in order to measure detailed chemical abundance patterns. We make use of both new observations with the WIYN-Hydra and Magellan-MIKE spectrographs, and also archival data from VLT-FLAMES. We measure the abundances of several light odd-Z, alpha, Fe-peak, and neutron-capture elements, and compare the bulge globular cluster patterns with those in halo clusters and the bulge field. C.I.J. acknowledges support through the Clay Fellowship administered by the Smithsonian Astrophysical Observatory.

  3. 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. PMID:25849493

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

    SciTech Connect

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

    2015-03-30

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

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

    DOE PAGESBeta

    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

  6. Folding of a large protein at high structural resolution.

    PubMed

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

    2013-11-19

    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

  7. 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

  8. 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.

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

    NASA Technical Reports Server (NTRS)

    Anderson, Scott F.

    2003-01-01

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

  10. 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

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

    PubMed Central

    Gao, Mu; Skolnick, Jeffrey

    2013-01-01

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

  12. Field star interactions with globular clusters

    NASA Astrophysics Data System (ADS)

    Peng, Wei

    1992-09-01

    We investigate a new interaction of globular clusters with galactic field stars. By dynamical friction, high-velocity field stars passing through individual globular clusters are decelerated. This frictional interaction contributes to cluster heating, and, in conjunction with disk shocking and other mechanisms, it helps regulate the evolution of globular clusters. Moreover, penetrating field stars with low relative velocities can even be captured by globular clusters. Our calculated rate of captures suggest that there is a substantial population of stars having an origin external to the globulars in which they now reside. Intriguing candidates for this 'immigrant' population include some blue straggler stars and short-period pulsars.

  13. HUBBLE SPIES GLOBULAR CLUSTER IN NEIGHBORING GALAXY

    NASA Technical Reports Server (NTRS)

    2002-01-01

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

  14. No energy equipartition in globular clusters

    NASA Astrophysics Data System (ADS)

    Trenti, Michele; van der Marel, Roeland

    2013-11-01

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

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

    PubMed Central

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

    1996-01-01

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

  16. The Ages of Globular Clusters

    NASA Astrophysics Data System (ADS)

    McNamara, D. H.

    2001-03-01

    We examine the luminosity levels of the main-sequence turnoffs, MTOv, and horizontal branches, Mv(HB), in 16 globular clusters. An entirely new approach of inferring the luminosity levels by utilizing high-amplitude δ Scuti variables (HADS) is introduced. When the MTOv values are compared with theoretical values inferred from models, we find all 16 clusters (metal-strong to metal-poor) are coeval with an average age of ~11.3 Gyr. A considerable scatter of Mv(HB) values of clusters at similar [Fe/H] values is found. A trend for clusters with blue horizontal branches to have brighter Mv(HB) than clusters with blue-red horizontal branches is suggested by the data. The Mv(HB) values appear to depend on another or other parameters in addition to the [Fe/H] values. In spite of this problem, we derive an equation relating Mv(HB) values of globular clusters to their [Fe/H] values. We also derive an equation relating the MTOv values of clusters to their [Fe/H] values. Both of these equations can be utilized to find cluster distances. The distance modulus of the LMC is found to be 18.66 from the VTO values of three LMC globular clusters; RR Lyrae stars in seven globular clusters yield 18.61, and RR Lyrae stars in the LMC bar yield 18.64.

  17. Hepatitis B virus large surface protein: function and fame

    PubMed Central

    Churin, Yuri; Roderfeld, Martin

    2015-01-01

    Chronic infection with hepatitis B virus (HBV) is the leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. HBV life cycle begins with viral attachment to hepatocytes, mediated by the large HBV surface protein (LHBs). Identification of the sodium-taurocholate cotransporting polypeptide (NTCP) as a HBV receptor has revealed a suitable target for viral entry inhibition. Analysis of serum hepatitis B surface antigen (HBsAg) level is a non-invasive diagnostic parameter that improves HBV treatment opportunities. Furthermore, HBsAg plays an important role in manipulation of host immune response by HBV. However, observations in patients with chronic hepatitis B under conditions of immune suppression and in transgenic mouse models of HBV infection suggest, that in absence of adaptive immune responses cellular mechanisms induced by HBV may also lead to the development of liver diseases. Thus, the multifaceted pathological aspects of HBsAg predetermine the design of new therapeutical options modulating associated biological implications. PMID:25713800

  18. Hepatitis B virus large surface protein: function and fame.

    PubMed

    Churin, Yuri; Roderfeld, Martin; Roeb, Elke

    2015-02-01

    Chronic infection with hepatitis B virus (HBV) is the leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. HBV life cycle begins with viral attachment to hepatocytes, mediated by the large HBV surface protein (LHBs). Identification of the sodium-taurocholate cotransporting polypeptide (NTCP) as a HBV receptor has revealed a suitable target for viral entry inhibition. Analysis of serum hepatitis B surface antigen (HBsAg) level is a non-invasive diagnostic parameter that improves HBV treatment opportunities. Furthermore, HBsAg plays an important role in manipulation of host immune response by HBV. However, observations in patients with chronic hepatitis B under conditions of immune suppression and in transgenic mouse models of HBV infection suggest, that in absence of adaptive immune responses cellular mechanisms induced by HBV may also lead to the development of liver diseases. Thus, the multifaceted pathological aspects of HBsAg predetermine the design of new therapeutical options modulating associated biological implications. PMID:25713800

  19. Redistribution of the discs large tumor suppressor protein during mitosis.

    PubMed

    Massimi, Paola; Gardiol, Daniela; Roberts, Sally; Banks, Lawrence

    2003-11-01

    Drosophila discs large (Dlg) has been shown to be an essential regulator of cell polarity and attachment, and is classified as a potential tumour suppressor in higher eukaryotes. Human Dlg is expressed in epithelial cells at sites of cell-cell contact and acts as a negative regulator of cell growth. Although hDlg has been shown to be phosphorylated during mitosis, little is known about its activity during this stage of the cell cycle. To investigate this further we have analysed in detail the pattern of hDlg expression during mitotic cell division. In early mitosis there is a marked increase in membrane-bound hDlg which is then retained throughout mitosis, while during cytokinesis, there is a specific concentration of hDlg at the midbody. Using mutants of Dlg we show that this is mediated by sequences in the carboxy terminal region of Dlg, but it does not require the SH3 or PDZ domains, and is independent of binding to protein 4.1. Finally, using a mutant of Dlg that consists of just this carboxy terminal region of the protein, we show that it can compete with endogenous hDlg for midbody accumulation, and this mutant also gives rise to altered cell growth. We conclude that localisation of Dlg to the midbody indicates a role for Dlg at this critical point in cytokinesis. PMID:14567986

  20. 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. PMID:26325310

  1. 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

  2. [Comparison of dynamic properties of various globular proteins and polyglutamic acid in alpha-helical and coil states. Rayleigh scattering of Mossbauer radiation data].

    PubMed

    Krupianskiĭ, Iu F; Kurinov, I V; Kuznetsov, S A; Eshchenko, G V; Gol'danskiĭ, V I

    1997-01-01

    Classical model system: Poly-L-glutamic acid (Poly-Glu) was investigated in a disordered coil state (at pH-7.0) and in helix state (at pH 2.0) by Rayleigh scattering of Moessbauer radiation technique. Consider that the coil state of poly-Glu models unfolded (random coil) state and alpha-helix state models the fluctuating secondary structure (during consequent folding of protein) comparative analysis of dynamical properties of poly-Glu in different states with dynamical properties of different proteins in native state (alpha-helical myoglobin and HSA, partially beta-sheet lysozyme) and in intermediate (molten globule) state (alpha-lactalbumin) was performed. This comparison bring some surprising results: native alpha-helical proteins behave itself close to random coil, native partially beta-sheet protein behaves close to fluctuating secondary structure (alpha-helix) and the dynamic behaviour of molten globule state (partially beta-sheet alpha-lactalbumin) is not different from those behaviour of lysozyme and much more rigid than native alpha-helical proteins. As a result one cannot exclude the possibility that folding process and dynamical properties at different steps of the folding are very different for alpha-helical and beta-sheet proteins. PMID:9181800

  3. Large-Scale Biophysical Evaluation of Protein PEGylation Effects: In Vitro Properties of 61 Protein Entities.

    PubMed

    Vernet, Erik; Popa, Gina; Pozdnyakova, Irina; Rasmussen, Jakob E; Grohganz, Holger; Giehm, Lise; Jensen, Malene H; Wang, Huabing; Plesner, Bitten; Nielsen, Hanne M; Jensen, Knud J; Berthelsen, Jens; Sundström, Michael; van de Weert, Marco

    2016-05-01

    PEGylation is the most widely used method to chemically modify protein biopharmaceuticals, but surprisingly limited public data is available on the biophysical effects of protein PEGylation. Here we report the first large-scale study, with site-specific mono-PEGylation of 15 different proteins and characterization of 61 entities in total using a common set of analytical methods. Predictions of molecular size were typically accurate in comparison with actual size determined by size-exclusion chromatography (SEC) or dynamic light scattering (DLS). In contrast, there was no universal trend regarding the effect of PEGylation on the thermal stability of a protein based on data generated by circular dichroism (CD), differential scanning calorimetry (DSC), or differential scanning fluorimetry (DSF). In addition, DSF was validated as a fast and inexpensive screening method for thermal unfolding studies of PEGylated proteins. Multivariate data analysis revealed clear trends in biophysical properties upon PEGylation for a subset of proteins, although no universal trends were found. Taken together, these findings are important in the consideration of biophysical methods and evaluation of second-generation biopharmaceutical drug candidates. PMID:27043713

  4. 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

  5. Large-scale protein-protein interactions detection by integrating big biosensing data with computational model.

    PubMed

    You, Zhu-Hong; Li, Shuai; Gao, Xin; Luo, Xin; Ji, Zhen

    2014-01-01

    Protein-protein interactions are the basis of biological functions, and studying these interactions on a molecular level is of crucial importance for understanding the functionality of a living cell. During the past decade, biosensors have emerged as an important tool for the high-throughput identification of proteins and their interactions. However, the high-throughput experimental methods for identifying PPIs are both time-consuming and expensive. On the other hand, high-throughput PPI data are often associated with high false-positive and high false-negative rates. Targeting at these problems, we propose a method for PPI detection by integrating biosensor-based PPI data with a novel computational model. This method was developed based on the algorithm of extreme learning machine combined with a novel representation of protein sequence descriptor. When performed on the large-scale human protein interaction dataset, the proposed method achieved 84.8% prediction accuracy with 84.08% sensitivity at the specificity of 85.53%. We conducted more extensive experiments to compare the proposed method with the state-of-the-art techniques, support vector machine. The achieved results demonstrate that our approach is very promising for detecting new PPIs, and it can be a helpful supplement for biosensor-based PPI data detection. PMID:25215285

  6. 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. PMID:26157115

  7. A large volume flat coil probe for oriented membrane proteins.

    PubMed

    Gor'kov, Peter L; Chekmenev, Eduard Y; Fu, Riqiang; Hu, Jun; Cross, Timothy A; Cotten, Myriam; Brey, William W

    2006-07-01

    15N detection of mechanically aligned membrane proteins benefits from large sample volumes that compensate for the low sensitivity of the observe nuclei, dilute sample preparation, and for the poor filling factor arising from the presence of alignment plates. Use of larger multi-tuned solenoids, however, is limited by wavelength effects that lead to inhomogeneous RF fields across the sample, complicating cross-polarization experiments. We describe a 600 MHz 15N-1H solid-state NMR probe with large (580 mm3) RF solenoid for high-power, multi-pulse sequence experiments, such as polarization inversion spin exchange at the magic angle (PISEMA). In order to provide efficient detection for 15N, a 4-turn solenoidal sample coil is used that exceeds 0.27 lambda at the 600 MHz 1H resonance. A balanced tuning-matching circuit is employed to preserve RF homogeneity across the sample for adequate magnetization transfer from 1H to 15N. We describe a procedure for optimization of the shorted 1/4 lambda coaxial trap that allows for the sufficiently strong RF fields in both 1H and 15N channels to be achieved within the power limits of 300 W 1H and 1 kW 15N amplifiers. The 8 x 6 x 12 mm solenoid sustains simultaneous B1 irradiation of 100 kHz at 1H frequency and 51 kHz at 15N frequency for at least 5 ms with 265 and 700 W of input power in the respective channels. The probe functionality is demonstrated by 2D 15N-1H PISEMA spectroscopy for two applications at 600 MHz. PMID:16580852

  8. Temporal Variant Frontotemporal Dementia Is Associated with Globular Glial Tauopathy

    PubMed Central

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

    2015-01-01

    Frontotemporal dementia (FTD) is a clinically and pathologically heterogeneous neurodegenerative disorder associated with atrophy of the frontal and temporal lobes. Most patients with focal temporal lobe atrophy present with either the semantic dementia subtype of FTD or the behavioral variant subtype. For patients with temporal variant FTD, the most common cause found on post-mortem examination has been a TDP-43 (transactive response DNA-binding protein 43 kDa) proteinopathy, but tauopathies have also been described, including Pick’s disease and mutations in the microtubule-associated protein tau (MAPT) gene. We report the clinical and imaging features of 2 patients with temporal variant FTD associated with a rare frontotemporal lobar degeneration pathology known as globular glial tauopathy. The pathologic diagnosis of globular glial tauopathy should be considered in patients with temporal variant FTD, particularly those who have atypical semantic dementia or an atypical parkinsonian syndrome in association with the right temporal variant. PMID:26102999

  9. Large-scale proteomic analysis of membrane proteins

    SciTech Connect

    Ahram, Mamoun; Springer, David L.

    2004-10-01

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

  10. Analysis of the code relating sequence to conformation in globular proteins. Development of a stereochemical alphabet on the basis of intra-residue information

    PubMed Central

    Robson, Barry; Pain, Roger H.

    1974-01-01

    1. The relation of primary sequence to all residue backbone conformations was explored to test out starting conformations for protein folding. 2. Information theory was used to obtain measures of information which quantitate the role of each residue in determining its own conformation; i.e. intra-residue information. 3. The information measures are plotted as a function of ϕ, ψ peptide-backbone angles and ϕ, ψ contour maps obtained for each of the 20 amino acids. These show characteristic differences between residues. 4. To find practical ways of relating sequence to ϕ, ψ angles, several types of stereochemical alphabet were investigated. The value of these was tested by using them to predict the ϕ, ψ angles of nine different proteins. 5. A difference plot was constructed to show regions of the sequence that require little or no information extra to the intra-residue information in order to predict a correct conformation. These regions are suggested to be candidates for nucleating sites in the protein. PMID:4463966

  11. 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.

  12. X-ray diagnostics of globular clusters

    NASA Technical Reports Server (NTRS)

    Grindlay, J. E.

    1982-01-01

    The presence of compact X-ray sources in globular clusters allows diagnostic studies of both the X-ray sources themselves and the globular clusters to be carried out. A review of much of this work, primarily based on Einstein X-ray observations and supporting studies of globular clusters at radio through UV wavelengths, is presented. The compact X-ray sources in globular clusters are found to be compact binaries containing neutron stars and - in a separate lower luminosity component of an apparently bimodal luminosity function - possibly white dwarfs. Implications for the formation and evolution of compact binary X-ray sources in globular clusters and in the galactic bulge are discussed. In particular, new evidence is presented that the galactic bulge sources may be compact binaries in the remnants of disrupted globular clusters.

  13. The globular cluster system of NGC 5128

    NASA Astrophysics Data System (ADS)

    Woodley, Kristin Anne

    2010-11-01

    The globular cluster system of a nearby giant elliptical galaxy, NGC 5128 is studied to place constraints on the formation history of the galaxy. In this thesis, we have identified 190 new globular clusters via radial velocity measurements, bringing the total known population of globular clusters to 605 within this galaxy. We have examined the colour and spatial distributions of the globular cluster system and find it is bimodal in colour, with both a red and blue globular cluster population. The blue population is more spatially extended than the red, and both populations fall off in number density with radius as a power-law. There is a clear lack of globular clusters along the isophotal minor axis of the galaxy beyond a galactocentric radius of 15' warranting further search. With this new dataset, we have measured the ages, metallicities, and formation timescales for 72 globular clusters. The spectroscopic metallicity distribution function is bimodal indicating there is a metal-rich and metal-poor globular cluster population that corresponds to the red and blue globular clusters, respectively. We find the majority of both metal-rich (56%) and metal-poor (92%) globular clusters are older than 8 Gyr, comparable to the Milky Way globular cluster system. We do find a smaller fraction, 18% of our sample, are metal-rich globular clusters with ages younger than 5 Gyr, while the remaining globular clusters have intermediate ages between 5--8 Gyr. The formation times of these globular clusters, estimated by their alpha-to-iron abundance ratios, indicate they formed quickly, on a timescale similar to globular clusters in most spiral galaxies, but on slower timescales than those in some other giant elliptical galaxies. The kinematics of the full globular cluster system is analyzed, as well as for the metal-rich and metal-poor globular clusters separately, as a function of galactocentric radius. We find the metal-poor globular cluster system has a small rotation signature of

  14. Field star diffusion in globular clusters

    NASA Astrophysics Data System (ADS)

    Peng, Wei; Weisheit, Jon C.

    1992-10-01

    We investigate a new interaction of globular clusters with galactic field stars: the deceleration (by dynamical friction) of high-velocity field stars diffusing through individual globular clusters. This frictional interaction contributes to cluster heating and, in conjunction with disk shocking and other mechanisms, helps to regulate the evolution of globular clusters. Moreover, penetrating field stars of low relative velocity can even be captured by globular clusters. Our calculated rate of capture suggests that there is a modest population of stars having an origin external to the clusters in which they now reside. Intriguing candidates for this 'immigrant' population include some blue stragglers and short-period pulsars.

  15. Rotation and flattening of globular clusters

    NASA Technical Reports Server (NTRS)

    Fall, S. M.; Frenk, C. S.

    1985-01-01

    Methods for measuring globular cluster ellipticities and the results of such measurements are reviewed, and the processes that determine the shapes of globular clusters and the ways in which they change with time are discussed. The use of the virial tensor theorem to study the connection between the global rotation, velocity anisotropy, and the shape of a self-gravitating system is addressed, and the employment of N-body models to simulate the evolution of globular clusters with initially anisotropic velocity distributions is examined. The application of a simple evaporation model and Fokker-Planck integrations to study the two-body diffusion in globular clusters is reviewed.

  16. 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. PMID:25700885

  17. Lack of Energy Equipartition in Globular Clusters

    NASA Astrophysics Data System (ADS)

    Trenti, Michele

    2013-05-01

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  20. Large-scale analysis of phosphorylated proteins in maize leaf.

    PubMed

    Bi, Ying-Dong; Wang, Hong-Xia; Lu, Tian-Cong; Li, Xiao-Hui; Shen, Zhuo; Chen, Yi-Bo; Wang, Bai-Chen

    2011-02-01

    Phosphorylation is an ubiquitous regulatory mechanism governing the activity, subcellular localization, and intermolecular interactions of proteins. To identify a broad range of phosphoproteins from Zea mays, we enriched phosphopeptides from Zea mays leaves using titanium dioxide microcolumns and then extensively fractionated and identified the phosphopeptides by mass spectrometry. A total of 165 unique phosphorylation sites with a putative role in biological processes were identified in 125 phosphoproteins. Most of these proteins are involved in metabolism, including carbohydrate and protein metabolism. We identified novel phosphorylation sites on translation initiation factors, splicing factors, nucleolar RNA helicases, and chromatin-remodeling proteins such as histone deacetylases. Intriguingly, we also identified phosphorylation sites on several proteins associated with photosynthesis, and we speculate that these sites may be involved in carbohydrate metabolism or electron transport. Among these phosphoproteins, phosphoenolpyruvate carboxylase and NADH: nitrate reductase (NR) which catalyzes the rate-limiting and regulated step in the pathway of inorganic nitrogen assimilation were identified. A conserved phosphorylation site was found in the cytochrome b5 heme-binding domain of NADH: nitrate reductase, suggesting that NADH: nitrate reductase is phosphorylated by the same protein kinase or highly related kinases. These data demonstrate that the pathways that regulate diverse processes in plants are major targets of phosphorylation. PMID:21053013

  1. Using the Experimentally Determined Components of the Overall Rotational Diffusion Tensor to Restrain Molecular Shape and Size in NMR Structure Determination of Globular Proteins and Protein-Protein Complexes

    PubMed Central

    Ryabov, Yaroslav; Suh, Jeong-Yong; Grishaev, Alexander; Clore, G. Marius; Schwieters, Charles D.

    2009-01-01

    This paper describes an approach for making use of the components of the experimentally determined rotational diffusion tensor derived from NMR relaxation measurements in macomolecular structure determination. The parameters of the rotational diffusion tensor describe the shape and size of the macromolecule or macromolecular complex and are therefore complimentary to traditional NMR restraints. The structural information contained in the rotational diffusion tensor is not dissimilar to that present in the small angle region of the solution X-ray scattering profiles. We demonstrate the utility of rotational diffusion tensor restraints for protein structure refinement using the N-terminal domain of enzyme I (EIN) as an example and validate the results by solution small angle X-ray scattering. We also show how rotational diffusion tensor restraints can be used for docking complexes using the dimeric HIV-1 protease and the EIN-HPr complexes as examples. In the former case, the rotational diffusion tensor restraints are sufficient in their own right to determine the position of one subunit relative to another. In the latter case, rotational diffusion tensor restraints complemented by highly ambiguous distance restraints derived from chemical shift pertubation mapping and a hydrophobic contact potential are sufficient to correctly dock EIN to HPr. In each case, the cluster containing the lowest energy structure corresponds to the correct solution. PMID:19537713

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

    NASA Technical Reports Server (NTRS)

    Di Stefano, R.; Rappaport, S.

    1994-01-01

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

  3. 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

  4. Recent advances in large-scale protein interactome mapping.

    PubMed

    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

  5. Scaling approach to the folding kinetics of large proteins.

    PubMed

    Nelson, Erik D; Grishin, Nick V

    2006-01-01

    We study a nucleation-growth model of protein folding and extend it to describe larger proteins with multiple folding units. The model is of one of an extremely simple type in which amino acids are allowed just two states--either folded (frozen) or unfolded. Its energetics are heterogeneous and Gō-like, the energy being defined in terms of the number of atom-to-atom contacts that would occur between frozen amino acids in the native crystal structure of the protein. Each collective state of the amino acids is intended to represent a small free energy microensemble consisting of the possible configurations of unfolded loops, open segments, and free ends constrained by the cross-links that form between folded parts of the molecule. We approximate protein free energy landscapes by an infinite subset of these microensemble topologies in which loops and open unfolded segments can be viewed roughly as independent objects for the purpose of calculating their entropy, and we develop a means to implement this approximation in Monte Carlo simulations. We show that this approach describes transition state structures (phi values) more accurately and identifies folding intermediates that were unavailable to previous versions of the model that restricted the number of loops and nuclei. PMID:16486182

  6. 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.

  7. 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).

  8. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  10. 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.

  11. Interdependence of the Rad50 hook and globular domain functions

    PubMed Central

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

    2015-01-01

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

  12. CENTRAL ROTATIONS OF MILKY WAY GLOBULAR CLUSTERS

    SciTech Connect

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

    2014-06-01

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

  13. X-ray binaries in globular clusters

    NASA Technical Reports Server (NTRS)

    Grindlay, Jonathan E.

    1988-01-01

    X-ray and optical studies of compact binaries and globular clusters are reviewed. Topics covered include, the formation of compact binaries by three-body interactions and by tidal capture, studies of the 11 minute binary in NGC 6624 and the 8.5 hour binary in M 15 (AC211), and an evolutionary model for compact binary formation. Optical searches for X-ray binaries in globular clusters are examined including CCD surveys and studies of NGC 6712. In addition, globular clusters with central cusps in their surface brightness profiles, questions concerning the blue color of binaries, diffuse line emission from CVs, and the possibility that X-ray burst sources in the galactic bulge were formed by tidal capture in globular clusters which have since been disrupted are discussed.

  14. Short-term X-ray variability of the globular cluster source 4U 1820 - 30 (NGC 6624)

    NASA Technical Reports Server (NTRS)

    Stella, L.; Kahn, S. M.; Grindlay, J. E.

    1984-01-01

    Analytical techniques for improved identification of the temporal and spectral variability properties of globular cluster and galactic bulge X-ray sources are described in terms of their application to a large set of observations of the source 4U 1820 - 30 in the globular cluster NGC 6624. The autocorrelation function, cross-correlations, time skewness function, erratic periodicities, and pulse trains are examined. The results are discussed in terms of current models with particular emphasis on recent accretion disk models. It is concluded that the analyzed observations provide the first evidence for shot-noise variability in a globular cluster X-ray source.

  15. 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.

  16. 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.

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

    SciTech Connect

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

    2010-03-11

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

  18. Charged states of proteins. Reactions of doubly protonated alkyldiamines with NH(3): solvation or deprotonation. Extension of two proton cases to multiply protonated globular proteins observed in the gas phase.

    PubMed

    Peschke, Michael; Blades, Arthur; Kebarle, Paul

    2002-09-25

    The apparent gas-phase basicities (GB(app)'s) of basic sites in multiply protonated molecules, such as proteins, can be approximately predicted. An approach used by Williams and co-workers was to develop an equation for a diprotonated system, NH(3)(CH(2))(7)NH(3)(2+), and then extend it with a summation of pairwise interactions to multiply protonated systems. Experimental determinations of the rates of deprotonation of NH(3)(CH(2))(7)NH(3)(2+) by a variety of bases B, in the present work, showed that GB(app) = GB(NH(3)) = 196 kcal/mol. This result is supported also by determinations of the equilibria: NH(3)(CH(2))(p)NH(3)(2+) + NH(3) = NH(3)(CH(2))(p)NH(3) x NH(3)(2+), for p = 7, 8, 10, 12. The described experimental GB(app) is 14 kcal/mol higher than the value predicted by the equation used by Williams and co-workers but in agreement with an ab initio result by Gronert. Equations based on electrostatics are developed for the two proton and multiproton systems which allow the evaluation of GB(app) of the basic sites on proteins. These are applied for the evaluation of GB(app) of the basic sites and of N(SB), the maximum number of protons that the nondenatured proteins, carbonic anhydrase (CAII), cytochrome c (CYC), and pepsin, can hold. The N(SB) values are compared with the observed charges, Z(obs)'s, when the nondenatured proteins are produced by electrospray and found in agreement with the proposal by de la Mora that Z(obs) is determined by the number of charges provided by the droplet that contains the protein, according to the charge residue model (CRM). The GB(app) values of proteins have many other applications. They can be compared with experimental measurements and are also needed for the understanding of the thermal denaturing of charged proteins and the thermal dissociation of charged protein complexes. PMID:12236767

  19. 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

  20. 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

  1. 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

  2. Central Dynamics of Globular Clusters

    NASA Astrophysics Data System (ADS)

    Noyola, Eva; Baumgardt, H.

    2007-12-01

    Globular clusters have historically been classified into two groups due to their dynamical state. They are considered to be either pre-core-collapse or post-core-collapse systems. Clusters are considered as post-core-collapse when they show concentrated surface brightness profiles, with a steep central cusp; while pre-core collapse clusters are less concentrated and have flat central cores. Recent observational results show that some clusters have central surface brightness profiles with intermediate central slopes, showing shallow cusps. These observations could be explained by the presence of a single or a binary intermediate mass black hole in the center of the clusters. In this work, we create realistic synthetic images from the output of N-body models. The images attempt to mock the resolution and point spread function of the high resolution cameras on board the Hubble Space Telescope. The models are created with and without central black holes, where the no black hole models are allowed to reach core-collapse. We measure surface brightness profiles both from integrated light and from star counts. From the profiles, we obtain parameters such as central surface brightness slope, core radius, and half light radius. We also test how well a King model describes each profile. We find that the black hole models produce shallow cusps if the black hole is larger than a certain mass; while models without central black holes produce more concentrated profiles. This approach, allows to make a thorough comparison between observations and models.

  3. 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

  4. 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

  5. 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. PMID:21836163

  6. Large-scale De Novo Prediction of Physical Protein-Protein Association*

    PubMed Central

    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

    2011-01-01

    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. PMID:21836163

  7. 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

  8. Ion exchange using poorly activated supports, an easy way for purification of large proteins.

    PubMed

    Pessela, Benevides C C; Munilla, Roberto; Betancor, Lorena; Fuentes, Manuel; Carrascosa, Alfonso V; Vian, Alejandro; Fernandez-Lafuente, Roberto; Guisán, Jose M

    2004-04-23

    Ion-exchange chromatography using commercial ionic supports is a commonly used technique for protein purification. However, selective adsorption of a target protein from a given extract onto commercial ion exchangers seems to be quite complex since they are designed to adsorb the maximum percentage of proteins with the opposite charge. In this paper, ion-exchanger supports with different activation degrees (from 1 to 40 micromol of amino groups per g of agarose) have been prepared and used for the purification of large proteins. These kinds of proteins have large surfaces to interact by many points with the support. Therefore, it was possible to purify large proteins as beta-galactosidase from Thermus sp. strain T2 from a crude extract from Escherichia coli or bovine liver catalase from a commercial preparation, with tailor-made ion-exchanger supports. A simple step of adsorption/desorption on lowly activated supports rendered both enzymes rather pure as confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Moreover, this strategy makes also easy the desorption step that requires rather low NaCl concentrations, which may become a serious problem for desorption of large proteins when using conventional supports, due to their ability of generating a very strong adsorption. PMID:15116925

  9. Health Benefits of Texturized Whey Proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. 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.

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

    SciTech Connect

    Cohen, Judith G.

    2011-10-20

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

  12. 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

  13. Red variables in globular clusters . Comparison with the Bulge and the LMC

    NASA Astrophysics Data System (ADS)

    Matsunaga, N.; Nakada, Y.; Tanabé, T.; Fukushi, H.; Ita, Y.

    We are conducting a project aimed at surveys and repeated observations of red variables (or long-period variables) in globular clusters. Using the IRSF/SIRIUS near-infrared facility located at South Africa, we are observing 145 globular clusters that are accessible from the site. In this contribution, we present our observations and preliminary results. We have discovered many red variables, especially in the Bulge region, whose memberships to the clusters remain to be confirmed. Using a sample of all red variables (both already known and newly discovered ones) in globular clusters except those projected to the Bulge region, we produce a log P-K diagram and compare it with those for the Bulge and the Large Magellanic Cloud. A prominent feature is that the bright part of overtone-pulsators' sequence (B+ and C\\prime) is absent. We discuss its implication on the evolution of red variables.

  14. 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.

  15. 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

  16. Stellar Populations Archive: The Globular Clusters

    NASA Astrophysics Data System (ADS)

    Zurek, D. R.; Ouellette, J. O.; Shara, M.; Hurley, J.; Ferguson, H.

    2001-12-01

    The Hubble Space Telescope cycle 10 panels have awarded us an archival grant to create a web based archive for the 101 Galactic globular clusters observed with WFPC2 on the Hubble Space Telescope. We will reduce all globular cluster WFPC2 data using ALLFrame in order to provide a photometric database which is precise and consistent from cluster to cluster. In addition the American Museum of Natural History has recently acquired three special purpose computers (GRAPE6) for dynamical simulations of stellar clusters. The simulations will be archived and a public database will be made available. The archive will go online early 2002 and as each cluster is reduced it will be made public. It is hoped that this "service to the community" will encourage comparitive studies of the Galactic globular cluster system. This database will also produce a library of template stellar populations with widespread applications.

  17. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.

    PubMed

    Kikuno, R; Nagase, T; Suyama, M; Waki, M; Hirosawa, M; Ohara, O

    2000-01-01

    HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb). In particular, cDNA clones capable of coding for large proteins (>50 kDa) are the current targets of the project. HUGE contains >1100 cDNA sequences and detailed information obtained through analysis of the sequences of cDNAs and the predicted proteins. Besides an increase in the number of cDNA entries, the amount of experimental data for expression profiling has been largely increased and data on chromosomal locations have been newly added. All of the protein-coding regions were examined by GeneMark analysis, and the results of a motif/domain search of each predicted protein sequence against the Pfam database have been newly added. HUGE is available through the WWW at http://www.kazusa.or.jp/huge PMID:10592264

  18. 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.

  19. 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

  20. Structure and Dynamics of the Globular Cluster Palomar 13

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  1. Small-scale batch crystallization of proteins revisited: an underutilized way to grow large protein crystals.

    PubMed

    Rayment, Ivan

    2002-02-01

    Growth of high-quality crystals is a major obstacle in many structural investigations. In recent years, the techniques for screening crystals have improved dramatically, whereas the methods for obtaining large crystals have progressed more slowly. This is an important issue since, although many structures can be solved from small crystals with synchrotron radiation, it is far easier to solve and refine structures when strong data is recorded from large crystals. In an effort to improve the size of crystals, a strategy for a small-scale batch method has been developed that in many cases yields far larger crystals than attainable by vapor diffusion. PMID:11839300

  2. 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

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

    PubMed

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

    2015-07-01

    Resources to mine the large amount of protein structures available today are necessary to better understand how amino acid variations are compatible with conformation preservation, to assist protein design, engineering and, further, the development of biologic therapeutic compounds. BCSearch is a versatile service to efficiently mine large collections of protein structures. It relies on a new approach based on a Binet-Cauchy kernel that is more discriminative than the widely used root mean square deviation criterion. It has statistics independent of size even for short fragments, and is fast. The systematic mining of large collections of structures such as the complete SCOPe protein structural classification or comprehensive subsets of the Protein Data Bank can be performed in few minutes. Based on this new score, we propose four innovative applications: BCFragSearch and BCMirrorSearch, respectively, search for fragments similar and anti-similar to a query and return information on the diversity of the sequences of the hits. BCLoopSearch identifies candidate fragments of fixed size matching the flanks of a gaped structure. BCSpecificitySearch analyzes a complete protein structure and returns information about sites having few similar fragments. BCSearch is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/BCSearch. PMID:25977292

  4. Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins.

    PubMed

    Sridhar, Settu; Nagamruta, Mallapragada; Guruprasad, Kunchur

    2015-01-01

    The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0-155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0-29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes. PMID:26465610

  5. Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins

    PubMed Central

    Sridhar, Settu; Nagamruta, Mallapragada; Guruprasad, Kunchur

    2015-01-01

    The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0–155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0–29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes. PMID:26465610

  6. 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.

  7. 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)

  8. 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

  9. 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

  10. Comprehensive characterization of protein 4.1 expression in epithelium of large intestine.

    PubMed

    Zhang, Jingxin; Yang, Shaomin; An, Chao; Wang, Jie; Yan, Hongxia; Huang, Yumin; Song, Jinlei; Yin, Changcheng; Baines, Anthony J; Mohandas, Narla; An, Xiuli

    2014-11-01

    The protein 4.1 family consists of four members, 4.1R, 4.1N, 4.1B and 4.1G, each encoded by a distinct gene. All 4.1 mRNAs undergo extensive alternative splicing. Functionally, they usually serve as adapters that link actin-based cytoskeleton to plasma membrane proteins. It has been reported that 4.1 proteins are expressed in most animal cell types and tissues including epithelial cells and epithelial tissues. However, the expression of 4.1 proteins in large intestine has not been well characterized. In the present study, we performed RT-PCR, western blot and immunohistochemistry analysis to characterize the transcripts, the protein expression and cellular localization of 4.1 proteins in the epithelia of mouse large intestine. We show that multiple transcripts derive from each gene, including eight 4.1R isoforms, four 4.1N isoforms, four 4.1B isoforms and six 4.1G isoforms. However, at the protein level, only one or two major bands were detected, implying that not all transcripts are translated and/or the proteins do not accumulate at detectable levels. Immunohistochemistry revealed that 4.1R, 4.1N and 4.1B are all expressed at the lateral membrane as well as cytoplasm of epithelial cells, suggesting a potentially redundant role of these proteins. Our findings not only provide new insights into the structure of protein 4.1 genes but also lay the foundation for future functional studies. PMID:24912669