WorldWideScience

Sample records for weakly bound structures

  1. Structure of the weakly bound triatomic He2Li and He2Na molecules

    Science.gov (United States)

    Suno, Hiroya

    2017-07-01

    We study the structure of triatomic molecules containing two helium atoms and one alkali-metal atom X (X = Li, Na). The three-body Schrödinger equation is solved in hyperspherical coordinates using the He-He and He-X pair van der Waals potentials available in the literature. We calculate the structural properties of the He2Li and He2Na bound states, and analyze one-dimensional pair and angle distribution functions as well as two-dimensional pair-pair and angle-angle distribution functions. These bound states are characterized by so peculiar weakly bound structures that classifying them into particular sizes and geometrical shapes appears to be elusive. Particularly, the JΠ=0+ excited states of He426Li and He427Li are found to constitute giant triatomic molecules with their size amounting to several hundred bohrs.

  2. Structure Effects in Collisions Induced by Halo and Weakly Bound Nuclei Around the Coulomb Barrier

    CERN Document Server

    Scuderi, V; Torresi, D; Fisichella, M; Borge, M J G; Randisi, G; Milin, M; Figuera, P; Raabe, R; Di Pietro, A; Amorini, F; Fraile, L M; Vidal, A M; Rizzo, F; Zadro, M; Gomez-Camacho, J; Pellegriti, M G; Papa, M; Jeppesen, H; Santonocito, D; Sanchez, E M R; Acosta, L; Tengblad, O; Lattuada, M; Musumarra, A; Scalia, G

    2010-01-01

    In this contribution, results concerning different reaction channels for the collisions induced by the three Be isotopes, Be-9,Be-10,Be-11, on a Zn-64 target at energies around the Coulomb barrier will be presented. The experiments with the radioactive Be-10,Be-11 beams were performed at REX-ISOLDE (CERN) whereas the experiment with the stable weakly bound Be-9 beam was performed at LNS Catania. Elastic scattering angular distributions have been measured for the three systems Be-9,Be-10,Be-11 + Zn-64 at the same center of mass energy. The angular distributions were analyzed with optical potentials and reaction cross sections were obtained from optical model calculations, performed with the code PTOLEMY. For the Be-11 + Zn-64 reaction, the break-up angular distribution was also measured.

  3. Dynamics of fragment capture for cluster structures of weakly bound 7Li

    Directory of Open Access Journals (Sweden)

    Shrivastava A.

    2013-12-01

    Full Text Available Role of cluster structures of 7Li on reaction dynamics have been studied by performing exclusive measurements of prompt-γ rays from residues with scattered particles at energy, E/Vb = 1.6, with 198Pt target. Yields of the residues resulting after capture of t and 4,5,6He, corresponding to different excitation energies of the composite system were estimated. The results were compared with three body classical-dynamical model for breakup fusion, constrained by the measured fusion, α and t capture cross-sections. The cross-section of residues from capture of α and t agreed well with the prediction of the model showing dominance of the two step process - breakup fusion, while those from tightly bound 6He showed massive transfer to be the dominant mechanism.

  4. Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals.

    Science.gov (United States)

    Pietrow, M; Gagoś, M; Misiak, L E; Kornarzyński, K; Szurkowski, J; Rochowski, P; Grzegorczyk, M

    2015-02-14

    It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra can be used as a probe indicating differences in the solid structures of hydrocarbons.

  5. Infrared spectroscopy of weakly bound molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, Lisa I-Ching

    1988-11-01

    The infrared spectra of a series of hydrated hydronium cluster ions and of protonated ethane ion are presented. A tandem mass spectrometer is ideally suited to obtaining the spectra of such weakly bound molecular ions. Traditional absorption spectroscopy is not feasible in these situations, so the techniques described in this thesis make use of some consequence of photon absorption with higher sensitivity than simply attenuation of laser power. That consequence is dissociation. By first mass selecting the parent ion under study and then mass selecting the fragment ion formed from dissociation, the near unit detection efficiency of ion counting methods has been used to full advantage.

  6. Weak Solution and Weakly Uniformly Bounded Solution of Impulsive Heat Equations Containing “Maximum” Temperature

    OpenAIRE

    Oyelami, Benjamin Oyediran

    2013-01-01

    In this paper, criteria for the existence of weak solutions and uniformly weak bounded solution of impulsive heat equation containing maximum temperature are investigated and results obtained. An example is given for heat flow system with impulsive temperature using maximum temperature simulator and criteria for the uniformly weak bounded of solutions of the system are obtained.

  7. Weak Solution and Weakly Uniformly Bounded Solution of Impulsive Heat Equations Containing “Maximum” Temperature

    Directory of Open Access Journals (Sweden)

    Oyelami, Benjamin Oyediran

    2013-09-01

    Full Text Available In this paper, criteria for the existence of weak solutions and uniformly weak bounded solution of impulsive heat equation containing maximum temperature are investigated and results obtained. An example is given for heat flow system with impulsive temperature using maximum temperature simulator and criteria for the uniformly weak bounded of solutions of the system are obtained.

  8. Electron Capture Dissociation of Weakly Bound Polypeptide Polycationic Complexes

    DEFF Research Database (Denmark)

    Haselmann, Kim F; Jørgensen, Thomas J D; Budnik, Bogdan A

    2002-01-01

    We have previously reported that, in electron capture dissociation (ECD), rupture of strong intramolecular bonds in weakly bound supramolecular aggregates can proceed without dissociation of weak intermolecular bonds. This is now illustrated on a series of non-specific peptide-peptide dimers...

  9. Inclusive breakup of three-fragment weakly bound nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Carlson, B.V.; Frederico, T. [Instituto Tecnológico de Aeronáutica, DCTA, 12.228-900 São José dos Campos, SP (Brazil); Hussein, M.S., E-mail: hussein@if.usp.br [Instituto Tecnológico de Aeronáutica, DCTA, 12.228-900 São José dos Campos, SP (Brazil); Instituto de Estudos Avançados, Universidade de São Paulo, C.P. 72012, 05508-970 São Paulo, SP (Brazil); Instituto de Física, Universidade de São Paulo, C.P. 66318, 05314-970 São Paulo, SP (Brazil)

    2017-04-10

    The inclusive breakup of three-fragment projectiles is discussed within a four-body spectator model. Both the elastic breakup and the non-elastic breakup are obtained in a unified framework. Originally developed in the 80's for two-fragment projectiles such as the deuteron, in this paper the theory is successfully generalized to three-fragment projectiles. The expression obtained for the inclusive cross section allows the extraction of the incomplete fusion cross section, and accordingly generalizes the surrogate method to cases such as (t, p) and (t, n) reactions. It is found that two-fragment correlations inside the projectile affect in a conspicuous way the elastic breakup cross section. The inclusive non-elastic breakup cross section is calculated and is found to contain the contribution of a three-body absorption term that is also strongly influenced by the two-fragment correlations. This latter cross section contains the so-called incomplete fusion where more than one compound nuclei are formed. Our theory describes both stable weakly bound three-fragment projectiles and unstable ones such as the Borromean nuclei.

  10. New error bounds for linear complementarity problems of weakly chained diagonally dominant B-matrices

    Directory of Open Access Journals (Sweden)

    Sun Deshu

    2017-07-01

    Full Text Available Some new error bounds for the linear complementarity problems are obtained when the involved matrices are weakly chained diagonally dominant B-matrices. Numerical examples are given to show the effectiveness of the proposed bounds.

  11. Intermolecular potential functions from spectroscopic properties of weakly bound complexes

    Energy Technology Data Exchange (ETDEWEB)

    Muenter, J.S.

    1992-01-01

    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  12. Model-Independent Analysis of $B \\to \\pi K$ Decays and Bounds on the Weak Phase $\\gamma$

    CERN Document Server

    Neubert, M

    1999-01-01

    A general parametrization of the amplitudes for the rare two-body decays B -> pi K is introduced, which makes maximal use of theoretical constraints arising from flavour symmetries of the strong interactions and the structure of the low-energy effective weak Hamiltonian. With the help of this parametrization, a model-independent analysis of the branching ratios and direct CP asymmetries in the various B -> pi K decay modes is performed, and the impact of hadronic uncertainties on bounds on the weak phase gamma = arg(Vub*) is investigated.

  13. Redshift-space limits of bound structures

    NARCIS (Netherlands)

    Duenner, Rolando; Reisenegger, Andreas; Meza, Andres; Araya, Pablo A.; Quintana, Hernan

    2007-01-01

    An exponentially expanding Universe, possibly governed by a cosmological constant, forces gravitationally bound structures to become more and more isolated, eventually becoming causally disconnected from each other and forming so-called 'island universes'. This new scenario reformulates the question

  14. Relativistic effects in the study of weakly bound F and Be nuclei

    Indian Academy of Sciences (India)

    FAHIME REZVANI

    2018-01-03

    Jan 3, 2018 ... Abstract. Relativistic effects are employed to describe the weakly bound nuclei of 17F and 11Be. In order to calculate the energy levels of the ground state and the excited states of these nuclei, we solved the Dirac equation with pseudospin symmetry in the shell model by using the basic concept of ...

  15. Relativistic effects in the study of weakly bound 17 F and 11 Be nuclei

    Indian Academy of Sciences (India)

    Relativistic effects are employed to describe the weakly bound nuclei of 17 F and 11 B e . In order to calculate the energy levels of the ground state and the excited states of these nuclei, we solved the Dirac equation with pseudospin symmetry in the shell model by using the basic concept of supersymmetric shape ...

  16. Shell-model description of weakly bound and unbound nuclear states

    Energy Technology Data Exchange (ETDEWEB)

    Michel, N. [University of Tennessee, Department of Physics and Astronomy, Knoxville, TN (United States); Oak Ridge National Laboratory, Physics Division, Oak Ridge, TN (United States); Joint Institute for Heavy Ion Research, Oak Ridge, TN (United States); Nazarewicz, W. [University of Tennessee, Department of Physics and Astronomy, Knoxville, TN (United States); Oak Ridge National Laboratory, Physics Division, Oak Ridge, TN (United States); Warsaw University, Institute of Theoretical Physics, Warsaw (Poland); Ploszajczak, M.; Rotureau, J. [CEA/DSM-CNRS/IN2P3, Grand Accelerateur National d' Ions Lourds (GANIL), Caen (France)

    2005-09-01

    A consistent description of weakly bound and unbound nuclei requires an accurate description of the particle continuum properties when carrying out multiconfiguration mixing. This is the domain of the Gamow Shell Model (GSM) which is the multiconfigurational shell model in the complex k-plane formulated using a complete Berggren ensemble representing bound single-particle (s.p.) states, s.p. resonances, and non-resonant complex energy continuum states. We discuss the salient features of effective interactions in weakly bound systems and show selected applications of the GSM formalism to p-shell nuclei. Finally, a development of the new non-perturbative scheme based on Density Matrix Renormalization Group methods to select the most significant continuum configurations in GSM calculations is discussed shortly. (orig.)

  17. Photoassociation spectra and the validity of the dipole approximation for weakly bound dimers

    Science.gov (United States)

    Cocks, Daniel G.; Whittingham, Ian B.

    2010-03-01

    Photoassociation (PA) of ultracold metastable helium to the 2s2p manifold is theoretically investigated using a nonperturbative close-coupled treatment in which the laser coupling is evaluated without assuming the dipole approximation. The results are compared with our previous study [D. G. Cocks and I. B. Whittingham, Phys. Rev. A 80, 023417 (2009)], which makes use of the dipole approximation. The approximation is found to strongly affect the PA spectra because the photoassociated levels are weakly bound, and a similar impact is predicted to occur in other systems of a weakly bound nature. The inclusion of the approximation does not affect the resonance positions or widths; however, significant differences are observed in the background of the spectra and the maximum laser intensity at which resonances are discernible. Couplings not satisfying the dipole selection rule |J-1|⩽J'⩽|J+1| do not lead to observable resonances.

  18. Bounds on the number of bound states in the transfer matrix spectrum for some weakly correlated lattice models

    Energy Technology Data Exchange (ETDEWEB)

    O' Carroll, Michael [Departamento de Matematica Aplicada e Estatistica, ICMC-USP, C.P. 668,13560-970 Sao Carlos, Sao Paulo (Brazil)

    2012-07-15

    We consider the interaction of particles in weakly correlated lattice quantum field theories. In the imaginary time functional integral formulation of these theories there is a relative coordinate lattice Schroedinger operator H which approximately describes the interaction of these particles. Scalar and vector spin, QCD and Gross-Neveu models are included in these theories. In the weakly correlated regime H=H{sub o}+W where H{sub o}=-{gamma}{Delta}{sub l}, 0 < {gamma} Much-Less-Than 1 and {Delta}{sub l} is the d-dimensional lattice Laplacian: {gamma}={beta}, the inverse temperature for spin systems and {gamma}={kappa}{sup 3} where {kappa} is the hopping parameter for QCD. W is a self-adjoint potential operator which may have non-local contributions but obeys the bound Double-Vertical-Line W(x, y) Double-Vertical-Line Less-Than-Or-Slanted-Equal-To cexp ( -a( Double-Vertical-Line x Double-Vertical-Line + Double-Vertical-Line y Double-Vertical-Line )), a large: exp-a={beta}/{beta}{sub o}{sup (1/2)}({kappa}/{kappa}{sub o}) for spin (QCD) models. H{sub o}, W, and H act in l{sub 2}(Z{sup d}), d Greater-Than-Or-Slanted-Equal-To 1. The spectrum of H below zero is known to be discrete and we obtain bounds on the number of states below zero. This number depends on the short range properties of W, i.e., the long range tail does not increase the number of states.

  19. Role of nuclear couplings in the inelastic excitation of weakly-bound neutron-rich nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Dasso, C.H. [Niels Bohr Institute, Copenhagen (Denmark); Lenzi, S.M.; Vitturi, A. [Universita di Padova (Italy)

    1996-12-31

    Much effort is presently devoted to the study of nuclear systems far from the stability line. Particular emphasis has been placed in light systems such as {sup 11}Li, {sup 8}B and others, where the very small binding energy of the last particles causes their density distribution to extend considerably outside of the remaining nuclear core. Some of the properties associated with this feature are expected to characterize also heavier systems in the vicinity of the proton or neutron drip lines. It is by now well established that low-lying concentrations of multipole strength arise from pure configurations in which a peculiar matching between the wavelength of the continuum wavefunction of the particles and the range of the weakly-bound hole states occurs. To this end the authors consider the break-up of a weakly-bound system in a heavy-ion collision and focus attention in the inelastic excitation of the low-lying part of the continuum. They make use of the fact that previous investigations have shown that the multipole response in this region is not of a collective nature and describe their excited states as pure particle-hole configurations. Since the relevant parameter determining the strength distributions is the binding energy of the last bound orbital they find it most convenient to use single-particle wavefunctions generated by a sperical square-well potential with characteristic nuclear dimensions and whose depth has been adjusted to give rise to a situation in which the last occupied neutron orbital is loosely-bound. Spin-orbit couplings are, for the present purpose, ignored. The results of this investigation clearly indicate that nuclear couplings have the predominant role in causing projectile dissociation in many circumstances, even at bombarding energies remarkably below the Coulomb barrier.

  20. Universal efficiency bounds of weak-dissipative thermodynamic cycles at the maximum power output.

    Science.gov (United States)

    Guo, Juncheng; Wang, Junyi; Wang, Yuan; Chen, Jincan

    2013-01-01

    Based on the assumption of weak dissipation introduced by Esposito et al. [Phys. Rev. Lett. 105, 150603 (2010)], analytic expressions for the efficiency bounds of several classes of typical thermodynamic cycles at the maximum power output are derived. The results obtained are of universal significance. They can be used to conveniently reveal the general characteristics of not only Carnot heat engines, but also isothermal chemical engines, non-Carnot heat engines, flux flow engines, gravitational engines, quantum Carnot heat engines, and two-level quantum Carnot engines at the maximum power output and to directly draw many important conclusions in the literature.

  1. Nuclear structure of weakly bound radioactive nuclei through elastic and and inelastic scattering on proton. Impacts of the couplings induced by these exotic nuclei on direct reactions; Structure de noyaux radioactifs faiblement lies par diffusions elastiques et inelastiques sur proton. Effets des couplages induits par ces noyaux exotiques sur les reactions directes

    Energy Technology Data Exchange (ETDEWEB)

    Lapoux, V

    2005-09-15

    Information on the structure, spectroscopy and target interaction potentials of exotic nuclei can be inferred by interpreting measured data from direct reactions on proton such as elastic or inelastic scattering of proton (p,p') or one-nucleon transfer reaction (p,d). A series of experimental results has been obtained at the GANIL facilities on the setting composed of the MUST telescope array used for the detection of light charged-particles and of CATS beam detectors. This setting aims at measuring reactions on light proton or deuteron targets through reverse kinematics. Particularly, results on C{sup 10}, C{sup 11} and on direct reactions with the He{sup 8} beam of Spiral are presented. The first chapter is dedicated to the description of the most important theories concerning the nucleus. The experimental tools used to probe the nucleus are reported in the second chapter. The third and fourth chapters present the framework that has allowed us to analyse results from (p,p') and (p,d) reactions on weakly bound exotic nuclei. The last chapter is dedicated to the description of future experimental programs. (A.C.)

  2. Coherent structures in wall-bounded turbulence.

    Science.gov (United States)

    Dennis, David J C

    2015-01-01

    The inherent difficulty of understanding turbulence has led to researchers attacking the topic in many different ways over the years of turbulence research. Some approaches have been more successful than others, but most only deal with part of the problem. One approach that has seen reasonable success (or at least popularity) is that of attempting to deconstruct the complex and disorganised turbulent flow field into to a set of motions that are in some way organised. These motions are generally called "coherent structures". There are several strands to this approach, from identifying the coherent structures within the flow, defining their characteristics, explaining how they are created, sustained and destroyed, to utilising their features to model the turbulent flow. This review considers research on coherent structures in wall-bounded turbulent flows: a class of flow which is extremely interesting to many scientists (mainly, but not exclusively, physicists and engineers) due to their prevalence in nature, industry and everyday life. This area has seen a lot of activity, particularly in recent years, much of which has been driven by advances in experimental and computational techniques. However, several ideas, developed many years ago based on flow visualisation and intuition, are still both informative and relevant. Indeed, much of the more recent research is firmly indebted to some of the early pioneers of the coherent structures approach. Therefore, in this review, selected historical research is discussed along with the more contemporary advances in an attempt to provide the reader with a good overview of how the field has developed and to highlight the perspicacity of some of the early researchers, as well as providing an overview of our current understanding of the role of coherent structures in wall-bounded turbulent flows.

  3. Coherent structures in wall-bounded turbulence

    Directory of Open Access Journals (Sweden)

    David J.C. Dennis

    2015-06-01

    Full Text Available The inherent difficulty of understanding turbulence has led to researchers attacking the topic in many different ways over the years of turbulence research. Some approaches have been more successful than others, but most only deal with part of the problem. One approach that has seen reasonable success (or at least popularity is that of attempting to deconstruct the complex and disorganised turbulent flow field into to a set of motions that are in some way organised. These motions are generally called "coherent structures". There are several strands to this approach, from identifying the coherent structures within the flow, defining their characteristics, explaining how they are created, sustained and destroyed, to utilising their features to model the turbulent flow. This review considers research on coherent structures in wall-bounded turbulent flows: a class of flow which is extremely interesting to many scientists (mainly, but not exclusively, physicists and engineers due to their prevalence in nature, industry and everyday life. This area has seen a lot of activity, particularly in recent years, much of which has been driven by advances in experimental and computational techniques. However, several ideas, developed many years ago based on flow visualisation and intuition, are still both informative and relevant. Indeed, much of the more recent research is firmly indebted to some of the early pioneers of the coherent structures approach. Therefore, in this review, selected historical research is discussed along with the more contemporary advances in an attempt to provide the reader with a good overview of how the field has developed and to highlight the perspicacity of some of the early researchers, as well as providing an overview of our current understanding of the role of coherent structures in wall-bounded turbulent flows.

  4. Bounding the Electromagnetic and Weak Dipole Moments of the Tau-Lepton in a Simplest Little Higgs Model

    Science.gov (United States)

    Gutiérrez-Rodríguez, A.

    From the total cross-section for the reaction e+e-→τ+τ-γ at the Z1 pole and in the framework of a simplest little Higgs model (SLHM), we get a limit on the characteristic energy scale of the model f, f ≥ 5.4 TeV, which in turn induces bounds on the electromagnetic and weak dipole moments of the tau-lepton. Our bounds on the electromagnetic moments are consistent with the bounds obtained by the L3 and OPAL collaborations for the reaction e+e-→τ+τ-γ. We also obtained bounds on the tau weak dipole moments which are consistent with the bounds obtained recently by the DELPHI and ALEPH collaborations from the reaction e+e-→τ+τ-.

  5. Structure Biology of Membrane Bound Enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Dax [Johns Hopkins Univ., Baltimore, MD (United States). School of Medicine. Dept. of Physiology

    2016-11-30

    The overall goal of the proposed research is to understand the membrane-associated active processes catalyzed by an alkane $\\square$-hydroxylase (AlkB) from eubacterium Pseudomonase oleovorans. AlkB performs oxygenation of unactivated hydrocarbons found in crude oils. The enzymatic reaction involves energy-demanding steps in the membrane with the uses of structurally unknown metal active sites featuring a diiron [FeFe] center. At present, a critical barrier to understanding the membrane-associated reaction mechanism is the lack of structural information. The structural biology efforts have been challenged by technical difficulties commonly encountered in crystallization and structural determination of membrane proteins. The specific aims of the current budget cycle are to crystalize AlkB and initiate X-ray analysis to set the stage for structural determination. The long-term goals of our structural biology efforts are to provide an atomic description of AlkB structure, and to uncover the mechanisms of selective modification of hydrocarbons. The structural information will help elucidating how the unactivated C-H bonds of saturated hydrocarbons are oxidized to initiate biodegradation and biotransformation processes. The knowledge gained will be fundamental to biotechnological applications to biofuel transformation of non-edible oil feedstock. Renewable biodiesel is a promising energy carry that can be used to reduce fossil fuel dependency. The proposed research capitalizes on prior BES-supported efforts on over-expression and purification of AlkB to explore the inner workings of a bioenergy-relevant membrane-bound enzyme.

  6. Recent developments in fusion and direct reactions with weakly bound nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Canto, L.F. [Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, 21941-972 Rio de Janeiro, RJ (Brazil); Instituto de Física, Universidade Federal Fluminense, Av. Litorânea S-N, 24210-340 Niteroi, RJ (Brazil); Gomes, P.R.S. [Instituto de Física, Universidade Federal Fluminense, Av. Litorânea S-N, 24210-340 Niteroi, RJ (Brazil); Donangelo, R. [Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, 21941-972 Rio de Janeiro, RJ (Brazil); Instituto de Física, Facultad de Ingeniería, C.C. 30, 11000 Montevideo (Uruguay); Lubian, J. [Instituto de Física, Universidade Federal Fluminense, Av. Litorânea S-N, 24210-340 Niteroi, RJ (Brazil); Hussein, M.S., E-mail: hussein@if.usp.br [Instituto de Estudos Avançados, Universidade de São Paulo, C.P. 72012, 05508-970, São Paulo, SP (Brazil); Departamento de Física Matemática, Instituto de Física, Universidade de São Paulo, C.P. 66318, 05314-970, São Paulo, SP (Brazil); Departamento de Física, Instituto Tecnológico de Aeronáutica, DCTA 12.228-900, São José dos Campos, SP (Brazil)

    2015-09-20

    In this Report we give a balanced account of the experimental and theoretical advances acquired over the last decade in the field of near-barrier fusion reactions induced by weakly bound stable and unstable nuclei. The elastic scattering and breakup reactions of these systems are also extensively reviewed as they play an important role in the fusion process. We review several theoretical tools used in the description of the data. The concepts of Complete Fusion (CF), Incomplete Fusion (ICF) and Total Fusion (TF), which is the sum of CF and ICF, are discussed and recent work on the calculation of these quantities is reviewed. The Continuum Discretized Coupled Channels (CDCC) method and its semiclassical version are described in detail and their limitations are pointed out. More importantly, we describe the salient features of the conclusions reached from the more than 40 measurements made, over a decade, of near-barrier fusion, elastic scattering and breakup reactions, and confront these data with the CDCC or other methods appropriate for these processes at the energy regime in question.

  7. Bounds on the Effect of Progressive Structural Degradation

    DEFF Research Database (Denmark)

    Achtziger, Wolfgang; Bendsøe, Martin P; Taylor, John E.

    1997-01-01

    Problem formulations are presented for the evaluation of upper and lower bounds on the effect of progressive structural degradation. For the purposes of this study, degradation effect is measured by an increase in global structural compliance (flexibility). Thus the stated bounds are given simply...

  8. Thermodynamic Upper Bound on Broadband Light Coupling with Photonic Structures

    KAUST Repository

    Yu, Zongfu

    2012-10-01

    The coupling between free space radiation and optical media critically influences the performance of optical devices. We show that, for any given photonic structure, the sum of the external coupling rates for all its optical modes are subject to an upper bound dictated by the second law of thermodynamics. Such bound limits how efficient light can be coupled to any photonic structure. As one example of application, we use this upper bound to derive the limit of light absorption in broadband solar absorbers. © 2012 American Physical Society.

  9. Coupled-channels effects in elastic scattering and near-barrier fusion induced by weakly bound nuclei and exotic halo nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Beck, C. [Institut Pluridisciplinaire Hubert Curien, UMR 7178, IN2P3-CNRS et Universite Louis Pasteur (Strasbourg I), 23 rue du Loess - BP28, F-67037 Strasbourg Cedex 2 (France); Keeley, N. [DSM/DAPNIA/SPhN CEA Saclay, Orme des Merisiers, F-91191 Gif-sur-Yvette Cedex (France); Diaz-Torres, A. [Department of Nuclear Physics, Research School of Physical Sciences and Engineering, The Australian National University, Canberra ACT 0200 (Australia)

    2007-03-15

    The influence on fusion of coupling to the breakup process is investigated for reactions where at least one of the colliding nuclei has a sufficiently low binding energy for breakup to become an important process. Elastic scattering, excitation functions for sub-and near-barrier fusion cross sections, and breakup yields are analyzed for {sup 6,7}Li+{sup 59}Co. Continuum-Discretized Coupled-Channels (CDCC) calculations describe well the data at and above the barrier. Elastic scattering with {sup 6}Li (as compared to {sup 7}Li) indicates the significant role of breakup for weakly bound projectiles. A study of {sup 4,6}He induced fusion reactions with a three-body CDCC method for the {sup 6}He halo nucleus is presented. The relative importance of breakup and bound-state structure effects on total fusion is discussed. (authors)

  10. Study of breakup and transfer of weakly bound nucleus 6Li to explore the low energy reaction dynamics

    Science.gov (United States)

    Zhang, G. L.; Zhang, G. X.; Hu, S. P.; Zhang, H. Q.; Gomes, P. R. S.; Lubian, J.; Guo, C. L.; Wu, X. G.; Yang, J. C.; Zheng, Y.; Li, C. B.; He, C. Y.; Zhong, J.; Li, G. S.; Yao, Y. J.; Guo, M. F.; Sun, H. B.; Valiente-Dobòn, J. J.; Goasduff, A.; Siciliano, M.; Galtarosa, F.; Francesco, R.; Testov, D.; Mengoni, D.; Bazzacco, D.; John, P. R.; Qu, W. W.; Wang, F.; Zheng, L.; Yu, L.; Chen, Q. M.; Luo, P. W.; Li, H. W.; Wu, Y. H.; Zhou, W. K.; Zhu, B. J.; Li, E. T.; Hao, X.

    2017-11-01

    Investigation of the breakup and transfer effect of weakly bound nuclei on the fusion process has been an interesting research topic in the past several years. However, owing to the low intensities of the presently available radioactive ion beam (RIB), it is difficult to clearly explore the reaction mechanisms of nuclear systems with unstable nuclei. In comparison with RIB, the beam intensities of stable weakly bound nuclei such as 6,7Li and 9Be, which have significant breakup probability, are orders of magnitude higher. Precise fusion measurements have already been performed with those stable weakly bound nuclei, and the effect of breakup of those nuclei on the fusion process has been extensively studied. Those nuclei indicated large production cross sections for particles other than the α + x breakup. The particles are originated from non-capture breakup (NCBU), incomplete fusion (ICF) and transfer processes. However, the conclusion of reaction dynamics was not clear and has the contradiction. In our previous experiments we have performed 6Li+96Zr and 154Sm at HI-13 Tandem accelerator of China Institute of Atomic Energy (CIAE) by using HPGe array. It is shown that there is a small complete fusion (CF) suppression on medium-mass target nucleus 96Zr different from about 35% suppression on heavier target nucleus 154Sm at near-barrier energies. It seems that the CF suppression factor depends on the charge of target nuclei. We also observed one neutron transfer process. However, the experimental data are scarce for medium-mass target nuclei. In order to have a proper understanding of the influence of breakup and transfer of weakly bound projectiles on the fusion process, we performed the 6Li+89Y experiment with incident energies of 22 MeV and 34 MeV on Galileo array in cooperation with Si-ball EUCLIDES at Legnaro National Laboratory (LNL) in Italy. Using particle-particle and particle-γ coincidences, the different reaction mechanisms can be clearly explored.

  11. Gamow shell-model description of weakly bound and unbound nuclear states

    Energy Technology Data Exchange (ETDEWEB)

    Michel, N.; Nazarewicz, W. [Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States); Ploszajczak, M.; Rotureau, J. [Grand Accelerateur National d' Ions Lourds (GANIL), CEA/DSM- NRS/IN2P3, BP 55027, F-14076 Caen Cedex 05 (France)

    2004-12-01

    Recently, the shell model in the complex k-plane (the so-called Gamow Shell Model) has been formulated using a complex Berggren ensemble representing bound single-particle states, single-particle resonances, and non-resonant continuum states. In this framework, we shall discuss binding energies and energy spectra of neutron-rich helium and lithium isotopes. The single-particle basis used is that of the Hartree-Fock potential generated self-consistently by the finite-range residual interaction. (Author) 21 refs., 5 tabs., 2 figs.

  12. Investigations of the potential functions of weakly bound diatomic molecules and laser-assisted excitive Penning ionization

    Energy Technology Data Exchange (ETDEWEB)

    Goble, J.H. Jr.

    1982-05-01

    Three variations on the Dunham series expansion function of the potential of a diatomic molecule are compared. The differences among these expansions lie in the choice of the expansion variable, lambda. The functional form of these variables are lambda/sub s/ = l-r/sub e//r for the Simon-Parr-Finlan version, lambda/sub T/ - 1-(r/sub e//r)/sup p/ for that of Thakkar, and lambda/sub H/ = 1-exp(-rho(r/r/sub e/-1) for that of Huffaker. A wide selection of molecular systems are examined. It is found that, for potentials in excess of thirty kcal/mole, the Huffaker expansion provides the best description of the three, extrapolating at large internuclear separation to a value within 10% of the true dissociation energy. For potentials that result from the interaction of excited states, all series expansions show poor behavior away from the equilibrium internuclear separation of the molecule. The series representation of the potentials of weakly bound molecules are examined in more detail. The ground states of BeAr/sup +/, HeNe/sup +/, NaAr, and Ar/sub 2/ and the excited states of HeNe+, NaNe, and NaAr are best described by the Thakkar expansion. Finally, the observation of laser-assisted excitive Penning ionization in a flowing afterglow is reported. The reaction Ar(/sup 3/P/sub 2/) + Ca + h nu ..-->.. Ar + Ca/sup +/(5p /sup 2/P/sub J/) + e/sup -/ occurs when the photon energy, h nu, is approximately equal to the energy difference between the metastable argon and one of the fine structure levels of the ion's doublet. By monitoring the cascade fluorescence of the above reaction and comparing it to the flourescence from the field-free process Ar(/sup 3/P/sub 2/) + Ca ..-->.. Ar + Ca/sup +/(4p /sup 2/P/sub J/) + e/sup -/ a surprisingly large cross section of 6.7 x 10/sup 3/ A/sup 2/ is estimated.

  13. Path integral Monte Carlo approach for weakly bound van der Waals complexes with rotations: algorithm and benchmark calculations.

    Science.gov (United States)

    Blinov, Nicholas; Song, XiaoGeng; Roy, Pierre-Nicholas

    2004-04-01

    A path integral Monte Carlo technique suitable for the treatment of doped helium clusters with inclusion of the rotational degrees of freedom of the dopant is introduced. The extrapolation of the results to the limit of infinite Trotter number is discussed in detail. Benchmark calculations for small weakly bound (4)He(N)--OCS clusters are presented. The Monte Carlo results are compared with those of basis set calculations for the He--OCS dimer. A technique to analyze the orientational imaginary time correlation function is suggested. It allows one to obtain information regarding the effective rotational constant for a doped helium cluster based on a model for the rotational Hamiltonian. The renormalization of the effective rotational constant for (4)He(N)--OCS clusters derived from the orientational imaginary time correlation function is in good agreement with experimental results.

  14. Vulnerable Derivatives and Good Deal Bounds: A Structural Model

    DEFF Research Database (Denmark)

    Murgoci, Agatha

    2013-01-01

    We price vulnerable derivatives -- i.e. derivatives where the counterparty may default. These are basically the derivatives traded on the over-the-counter (OTC) markets. Default is modeled in a structural framework. The technique employed for pricing is good deal bounds (GDBs). The method imposes...

  15. The limits of bound structures in the accelerating Universe

    NARCIS (Netherlands)

    Dunner, R; Araya, PA; Meza, A; Reisenegger, A

    2006-01-01

    According to the latest evidence, the Universe is entering an era of exponential expansion, where gravitationally bound structures will get disconnected from each other, forming isolated 'island universes'. In this scenario, we present a theoretical criterion to determine the boundaries of

  16. Bounds on the Effect of Progressive Structural Degradation

    DEFF Research Database (Denmark)

    Achtziger, W.; Bendsøe, Martin P; Taylor, John E.

    1998-01-01

    " interpretations. Several formulations for extremal "loss of stiffness", each with one or another form of model for local degradation, are compared and evaluated. An isoperimetric constraint controls the degree of loss in overall structural stiffness. Results obtained sequentially for a set of specified......Problem formulations are presented for the evaluation of upper and lower bounds on the effect of progressive structural degradation. For the purposes of this study, degradation effect is measured by an increase in global structural compliance (flexibility). Thus the slated bounds are given simply...... by the maximum and minimum values, respectively, of the increase in compliance corresponding to a specified global interval of degradation. Solutions to these optimization problems identify the particular patterns of local degradation associated with the respective "worst case" and "least degrading...

  17. The structure of weak shocks in quantum plasmas

    CERN Document Server

    Bychkov, Vitaly; Marklund, Mattias

    2008-01-01

    The structure of a weak shock in a quantum plasma is studied, taking into account both dissipation terms due to thermal conduction and dispersive quantum terms due to the Bohm potential. Unlike quantum systems without dissipations, even a small thermal conduction may lead to a stationary shock structure. In the limit of zero quantum effects, the monotonic Burgers solution for the weak shock is recovered. Still, even small quantum terms make the structure non-monotonic with the shock driving a train of oscillations into the initial plasma. The oscillations propagate together with the shock. The oscillations become stronger as the role of Bohm potential increases in comparison with thermal conduction. The results could be of importance for laser-plasma interactions, such as inertial confinement fusion plasmas, and in astrophysical environments, as well as in condensed matter systems.

  18. Calculations on the threshold anomaly of weakly bound projectiles with Sao Paulo and Woods-Saxon polarization potentials

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-Camacho, A; Aguilera, E F; Martinez-Quiroz, E [Departamento de Aceleradores, Instituto Nacional de Investigaciones Nucleares, Apartado Postal 18-1027, C.P. 11801, Mexico, D.F. (Mexico); Gomes, P R S; Lubian, J [Instituto de Fisica, Universidade Federal Fluminenese, Avenida Litoranea s/n, Gragoata, Niteroi, RJ, cep 24210-340 (Brazil); Canto, L F, E-mail: arturo.gomez@inin.gob.m [Instituto de Fisica, Universidade Federal do Rio de Janeiro, C.P. 68528, Rio de Janeiro, R.J., cep 21941-972 (Brazil)

    2010-07-01

    A thorough study of the energy dependence of the nuclear optical potential in reactions involving the weakly bound projectiles {sup 8}B, {sup 7}Be and {sup 6}Li on the target {sup 58}Ni and {sup 9}Be on {sup 27}Al is carried out by performing a {chi}{sup 2}-analysis of recent measurements of elastic scattering cross sections for energies around and above the Coulomb barrier. For this purpose two different potential types are used: the double folding Sao Paulo potential and the Woods-Saxon potential. The calculations performed for the energy dependence of the real and imaginary parts of the polarization potentials show that these potentials besides satisfying the dispersion relation, for some nuclear systems the uncertainties on the energy dependence of the polarization potentials allow to conclude that these systems present a behavior consistent with the Breakup Theshold Anomaly. In other cases, due to the large uncertainties, it is not possible to make a definitive conclusion about the anomalies.

  19. Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

    Energy Technology Data Exchange (ETDEWEB)

    Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de [Instituto de Física, Universidade de Brasília, 70910 Brasília (Brazil); Pirani, F. [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Aquilanti, V. [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Instituto de Física, Universidade Federal da Bahia, 40210 Salvador (Brazil); Gargano, R. [Instituto de Física, Universidade de Brasília, 70910 Brasília (Brazil); Departments of Chemistry and Physics, University of Florida, Quantum Theory Project, Gainesville, Florida 32611 (United States)

    2014-10-07

    We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry of the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.

  20. Structure and weak hydrogen bonds in liquid acetaldehyde

    Directory of Open Access Journals (Sweden)

    Cordeiro Maria A. M.

    2004-01-01

    Full Text Available Monte Carlo simulations have been performed to investigate the structure and hydrogen bonds formation in liquid acetaldehyde. An all atom model for the acetaldehyde have been optimized in the present work. Theoretical values obtained for heat of vaporisation and density of the liquid are in good agreement with experimental data. Graphics of radial distribution function indicate a well structured liquid compared to other similar dipolar organic liquids. Molecular mechanics minimization in gas phase leads to a trimer of very stable structure. The geometry of this complex is in very good agreement with the rdf. The shortest site-site correlation is between oxygen and the carbonyl hydrogen, suggesting that this correlation play a important role in the liquid structure and properties. The OxxxH average distance and the C-HxxxO angle obtained are characteristic of weak hydrogen bonds.

  1. Intermolecular potential functions from spectroscopic properties of weakly bound complexes. Third progress report, July 1, 1991--June 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Muenter, J.S.

    1992-08-01

    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  2. Structure of the δ-opioid receptor bound to naltrindole.

    Science.gov (United States)

    Granier, Sébastien; Manglik, Aashish; Kruse, Andrew C; Kobilka, Tong Sun; Thian, Foon Sun; Weis, William I; Kobilka, Brian K

    2012-05-16

    The opioid receptor family comprises three members, the µ-, δ- and κ-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The δ-opioid receptor (δ-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the µ-OR and κ-OR have recently been solved. Here we report the crystal structure of the mouse δ-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the µ-OR and κ-OR, the δ-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the δ-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.

  3. Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor.

    Science.gov (United States)

    Hurt, Darrell E; Widom, Joanne; Clardy, Jon

    2006-03-01

    Membrane-associated dihydroorotate dehydrogenase (DHODH) is an antimalarial therapeutic target without an effective inhibitor. Studies on human DHODH (HsDHODH) led to a structural mechanistic model in which respiratory quinones bind in a tunnel formed by the highly variable N-terminus that leads to the flavin mononucleotide-binding site. The therapeutic agents leflunomide (Arava) and brequinar sodium inhibit HsDHODH by binding in this tunnel. Plasmodium falciparum DHODH (PfDHODH) and HsDHODH have markedly different sensitivities to the two drugs. To understand the structural basis of this differential sensitivity and begin a structure-based drug-design cycle for PfDHODH inhibitors, the three-dimensional structure (2.4 Angstroms, R = 20.1%) of PfDHODH bound to the active metabolite of leflunomide was determined by X-ray crystallography. Comparison of the structures of HsDHODH and PfDHODH reveals a completely different binding mode for the same inhibitor in these two catalytically identical enzymes and explains the previously observed species-specific preferential binding. Because no effective inhibitors have been described for PfDHODH, this structure provides critical insight for the design of potential antimalarials.

  4. Structures of potent anticancer compounds bound to tubulin.

    Science.gov (United States)

    McNamara, Dan E; Senese, Silvia; Yeates, Todd O; Torres, Jorge Z

    2015-07-01

    Small molecules that bind to tubulin exert powerful effects on cell division and apoptosis (programmed cell death). Cell-based high-throughput screening combined with chemo/bioinformatic and biochemical analyses recently revealed a novel compound MI-181 as a potent mitotic inhibitor with heightened activity towards melanomas. MI-181 causes tubulin depolymerization, activates the spindle assembly checkpoint arresting cells in mitosis, and induces apoptotic cell death. C2 is an unrelated compound previously shown to have lethal effects on microtubules in tumorigenic cell lines. We report 2.60 Å and 3.75 Å resolution structures of MI-181 and C2, respectively, bound to a ternary complex of αβ-tubulin, the tubulin-binding protein stathmin, and tubulin tyrosine ligase. In the first of these structures, our crystallographic results reveal a unique binding mode for MI-181 extending unusually deep into the well-studied colchicine-binding site on β-tubulin. In the second structure the C2 compound occupies the colchicine-binding site on β-tubulin with two chemical moieties recapitulating contacts made by colchicine, in combination with another system of atomic contacts. These insights reveal the source of the observed effects of MI-181 and C2 on microtubules, mitosis, and cultured cancer cell lines. The structural details of the interaction between tubulin and the described compounds may guide the development of improved derivative compounds as therapeutic candidates or molecular probes to study cancer cell division. © 2015 The Protein Society.

  5. Structure of the [delta]-opioid receptor bound to naltrindole

    Energy Technology Data Exchange (ETDEWEB)

    Granier, Sébastien; Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Weis, William I.; Kobilka, Brian K. (Stanford-MED)

    2012-07-11

    The opioid receptor family comprises three members, the {mu}-, {delta}- and {kappa}-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The {delta}-opioid receptor ({delta}-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the {mu}-OR and {kappa}-OR have recently been solved. Here we report the crystal structure of the mouse {delta}-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the {mu}-OR and {kappa}-OR, the {delta}-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the {delta}-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.

  6. Computational structural analysis: multiple proteins bound to DNA.

    Directory of Open Access Journals (Sweden)

    Andrija Tomovic

    Full Text Available BACKGROUND: With increasing numbers of crystal structures of proteinratioDNA and proteinratioproteinratioDNA complexes publically available, it is now possible to extract sufficient structural, physical-chemical and thermodynamic parameters to make general observations and predictions about their interactions. In particular, the properties of macromolecular assemblies of multiple proteins bound to DNA have not previously been investigated in detail. METHODOLOGY/PRINCIPAL FINDINGS: We have performed computational structural analyses on macromolecular assemblies of multiple proteins bound to DNA using a variety of different computational tools: PISA; PROMOTIF; X3DNA; ReadOut; DDNA and DCOMPLEX. Additionally, we have developed and employed an algorithm for approximate collision detection and overlapping volume estimation of two macromolecules. An implementation of this algorithm is available at http://promoterplot.fmi.ch/Collision1/. The results obtained are compared with structural, physical-chemical and thermodynamic parameters from proteinratioprotein and single proteinratioDNA complexes. Many of interface properties of multiple proteinratioDNA complexes were found to be very similar to those observed in binary proteinratioDNA and proteinratioprotein complexes. However, the conformational change of the DNA upon protein binding is significantly higher when multiple proteins bind to it than is observed when single proteins bind. The water mediated contacts are less important (found in less quantity between the interfaces of components in ternary (proteinratioproteinratioDNA complexes than in those of binary complexes (proteinratioprotein and proteinratioDNA.The thermodynamic stability of ternary complexes is also higher than in the binary interactions. Greater specificity and affinity of multiple proteins binding to DNA in comparison with binary protein-DNA interactions were observed. However, protein-protein binding affinities are stronger in

  7. The structure of a market containing boundedly rational firms

    Science.gov (United States)

    Ibrahim, Adyda; Zura, Nerda; Saaban, Azizan

    2017-11-01

    The structure of a market is determined by the number of active firms in it. Over time, this number is affected by the exit of existing firms, called incumbents, and entries of new firms, called entrant. In this paper, we considered a market governed by the Cobb-Douglas utility function such that the demand function is isoelastic. Each firm is assumed to produce a single homogenous product under a constant unit cost. Furthermore, firms are assumed to be boundedly rational in adjusting their outputs at each period. A firm is considered to exit the market if its output is negative. In this paper, the market is assumed to have zero barrier-to-entry. Therefore, the exiting firm can reenter the market if its output is positive again, and new firms can enter the market easily. Based on these assumptions and rules, a mathematical model was developed and numerical simulations were run using Matlab. By setting certain values for the parameters in the model, initial numerical simulations showed that in the long run, the number of firms that manages to survive the market varies between zero to 30. This initial result is consistent with the idea that a zero barrier-to-entry may produce a perfectly competitive market.

  8. Structure of the agonist-bound neurotensin receptor.

    Science.gov (United States)

    White, Jim F; Noinaj, Nicholas; Shibata, Yoko; Love, James; Kloss, Brian; Xu, Feng; Gvozdenovic-Jeremic, Jelena; Shah, Priyanka; Shiloach, Joseph; Tate, Christopher G; Grisshammer, Reinhard

    2012-10-25

    Neurotensin (NTS) is a 13-amino-acid peptide that functions as both a neurotransmitter and a hormone through the activation of the neurotensin receptor NTSR1, a G-protein-coupled receptor (GPCR). In the brain, NTS modulates the activity of dopaminergic systems, opioid-independent analgesia, and the inhibition of food intake; in the gut, NTS regulates a range of digestive processes. Here we present the structure at 2.8 Å resolution of Rattus norvegicus NTSR1 in an active-like state, bound to NTS(8-13), the carboxy-terminal portion of NTS responsible for agonist-induced activation of the receptor. The peptide agonist binds to NTSR1 in an extended conformation nearly perpendicular to the membrane plane, with the C terminus oriented towards the receptor core. Our findings provide, to our knowledge, the first insight into the binding mode of a peptide agonist to a GPCR and may support the development of non-peptide ligands that could be useful in the treatment of neurological disorders, cancer and obesity.

  9. Weakly bound states of two- and three-boson systems in the crossover from two to three dimensions

    DEFF Research Database (Denmark)

    Yamashita, Marcelo; Bellotti, Filipe Furlan; Frederico, Tobias

    2015-01-01

    The spectrum and properties of quantum bound states is strongly dependent on the dimensionality of space. How this comes about and how one may theoretically and experimentally study the interpolation between different dimensions is a topic of great interest in different fields of physics. In this...

  10. Investigating the Mode Structure of the Weakly Coherent Mode

    Science.gov (United States)

    Golfinopoulos, T.; Labombard, B.; Hubbard, A.; Hughes, J. W.; Whyte, D.; Granetz, R.; Davis, E. M.; Edlund, E.; Ennever, P.; Greenwald, M.; Marmar, E.; Porkolab, M.; Wolfe, S. M.; Wukitch, S. J.; Alcator C-Mod Team

    2017-10-01

    The Weakly Coherent Mode (WCM, 200-500 kHz, k⊥ρs < 0.1) is an edge phenomenon associated with I-mode, a steady state, ELM-free confinement regime that has been observed on the Alcator C-Mod, ASDEX-Upgrade, and DIII-D tokamaks. I-mode is characterized by high particle flux, creating a separation of transport channels that leads to the development of a temperature pedestal, but not a density pedestal. The WCM is thought to contribute to this increased particle flux, though its precise role in regulating edge transport is not well-understood. Here, we investigate the structure of the WCM, particularly regarding poloidal asymmetry, using data from poloidally- and toroidally-arrayed Mirnov coils, as well as phase contrast imaging, with radial profiles of Te, ne, and Φ in the scrape-off layer provided by the Mirror Langmuir Probe. The WCM phenomenology is then compared to that of the Quasi-Coherent Mode, the edge fluctuation responsible for exhausting impurities in the Enhanced Dα H-mode. This work is supported by USDoE award DE-FC02-99ER54512.

  11. Crossing the Logarithmic Barrier for Dynamic Boolean Data Structure Lower Bounds

    OpenAIRE

    Larsen, Kasper Green; Weinstein, Omri; Yu, Huacheng

    2017-01-01

    This paper proves the first super-logarithmic lower bounds on the cell probe complexity of dynamic boolean (a.k.a. decision) data structure problems, a long-standing milestone in data structure lower bounds. We introduce a new method for proving dynamic cell probe lower bounds and use it to prove a $\\tilde{\\Omega}(\\log^{1.5} n)$ lower bound on the operational time of a wide range of boolean data structure problems, most notably, on the query time of dynamic range counting over $\\mathbb{F}_2$ ...

  12. Weak radiative decays of the B meson and bounds on M{sub H}± in the Two-Higgs-Doublet Model

    Energy Technology Data Exchange (ETDEWEB)

    Misiak, Mikolaj [University of Warsaw, Faculty of Physics, Institute of Theoretical Physics, Warsaw (Poland); CERN, Theoretical Physics Department, Geneva 23 (Switzerland); Steinhauser, Matthias [Karlsruhe Institute of Technology (KIT), Institut fuer Theoretische Teilchenphysik, Karlsruhe (Germany)

    2017-03-15

    In a recent publication (Abdesselam et al. arXiv:1608.02344), the Belle collaboration updated their analysis of the inclusive weak radiative B-meson decay, including the full dataset of (772 ± 11) x 10{sup 6} B anti B pairs. Their result for the branching ratio is now below the Standard Model prediction (Misiak et al. Phys Rev Lett 114:221801, 2015, Czakon et al. JHEP 1504:168, 2015), though it remains consistent with it. However, bounds on the charged Higgs boson mass in the Two-Higgs-Doublet Model get affected in a significant manner. In the so-called Model II, the 95% C.L. lower bound on M{sub H}± is now in the 570-800 GeV range, depending quite sensitively on the method applied for its determination. Our present note is devoted to presenting and discussing the updated bounds, as well as to clarifying several ambiguities that one might encounter in evaluating them. One of such ambiguities stems from the photon energy cutoff choice, which deserves re-consideration in view of the improved experimental accuracy. (orig.)

  13. Structure of weakly periodic rings with potent extended commutators

    OpenAIRE

    Adil Yaqub

    2001-01-01

    A well-known theorem of Jacobson (1964, page 217) asserts that a ring R with the property that, for each x in R, there exists an integer n(x)>1 such that xn(x)=x is necessarily commutative. This theorem is generalized to the case of a weakly periodic ring R with a “sufficient” number of potent extended commutators. A ring R is called weakly periodic if every x in R can be written in the form x=a+b, where a is nilpotent and b is “potent” in the sense that bn(b)=b for some integer n(b)>1. It is...

  14. Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

    Energy Technology Data Exchange (ETDEWEB)

    Simonetti, Angelita [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Marzi, Stefano [Architecture et Réactivité de l’ARN, UPR 9002 CNRS, IBMC (Institute of Molecular and Cellular Biology), 15 Rue R. Descartes, 67084 Strasbourg, France, Université de Strasbourg, 67000 Strasbourg (France); Fabbretti, Attilio [University of Camerino, 62032 Camerino (Monaco) (Italy); Hazemann, Isabelle; Jenner, Lasse [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale -INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Urzhumtsev, Alexandre [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Université de Lorraine, 54506 Vandoeuvre-lès-Nancy (France); Gualerzi, Claudio O. [University of Camerino, 62032 Camerino (Monaco) (Italy); Klaholz, Bruno P., E-mail: klaholz@igbmc.fr [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France)

    2013-06-01

    The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.

  15. Domain wall structure of weak ferromagnets according to Raman

    Energy Technology Data Exchange (ETDEWEB)

    Kuzmenko, A.P., E-mail: apk3527@mail.ru [South-West State University (Russian Federation); Abakumov, P.V. [South-West State University (Russian Federation); Dobromyslov, M.B. [Pacific State University (Russian Federation)

    2012-03-15

    Visualizing the domain structure and the fine structure of domain walls in orthoferrites based on Raman was proposed. The Raman mapping imaging was obtained for the straight and curved domain wall at line 221 cm{sup -1}. The parameters of the domain structure and wall obtained by Raman are consistent with magnetooptical measurements. - Highlights: Black-Right-Pointing-Pointer Visualizing the fine structure of domain walls in YFeO{sub 3} by Raman was proposed. Black-Right-Pointing-Pointer One was obtained for the straight and curved domain wall at line 221 cm{sup -1}. Black-Right-Pointing-Pointer The parameters of the domain structure and wall obtained are in accordance with other measurements.

  16. Weakly bound few-cluster structures with many-body correlations

    DEFF Research Database (Denmark)

    Hove, Dennis

    2017-01-01

    in nature, the focus of the method is on applications within nuclear physics. As such this method is applied to $^{26}$O, $^{72}$Ca, and $^{70}$Kr, all of which are topical, nuclear systems, each demonstrating particular applications of the method. The application to $^{26}\\text{O}$ demonstrates the ability...

  17. Nuclear structure of bound states of asymmetric dark matter

    Science.gov (United States)

    Gresham, Moira I.; Lou, Hou Keong; Zurek, Kathryn M.

    2017-11-01

    Models of asymmetric dark matter (ADM) with a sufficiently attractive and long-range force give rise to stable bound objects, analogous to nuclei in the Standard Model, called nuggets. We study the properties of these nuggets and compute their profiles and binding energies. Our approach, applicable to both elementary and composite fermionic ADM, utilizes relativistic mean field theory, and allows a more systematic computation of nugget properties, over a wider range of sizes and force mediator masses, compared to previous literature. We identify three separate regimes of nugget property behavior corresponding to (1) nonrelativistic and (2) relativistic constituents in a Coulomb-like limit, and (3) saturation in an anti-Coulomb limit when the nuggets are large compared to the force range. We provide analytical descriptions for nuggets in each regime. Through numerical calculations, we are able to confirm our analytic descriptions and also obtain smooth transitions for the nugget profiles between all three regimes. We also find that over a wide range of parameter space, the binding energy in the saturation limit is an O (1 ) fraction of the constituent's mass, significantly larger than expectations in the nonrelativistic case. In a companion paper, we apply our results to the synthesis of ADM nuggets in the early Universe.

  18. Lower bound plane stress element for modelling 3D structures

    DEFF Research Database (Denmark)

    Herfelt, Morten Andersen; Poulsen, Peter Noe; Hoang, Linh Cao

    2017-01-01

    In-plane action is often the primary load-carrying mechanism of reinforced concrete structures. The plate bending action will be secondary, and the behaviour of the structure can be modelled with a reasonable accuracy using a generalised three-dimensional plane stress element. In this paper...

  19. Structural features of free and covalently bound glycans

    NARCIS (Netherlands)

    Blanchard, Véronique

    2006-01-01

    Carbohydrates act in many cellular functions and biological processes such as cell-cell recognition and adhesion, inflammation, fertilization, signal transduction, and development. In this context, structural information is required to understand molecular mechanisms involving carbohydrates. The

  20. Three-dimensional structure of poliovirus receptor bound to poliovirus

    Science.gov (United States)

    Belnap, David M.; McDermott, Brian M.; Filman, David J.; Cheng, Naiqian; Trus, Benes L.; Zuccola, Harmon J.; Racaniello, Vincent R.; Hogle, James M.; Steven, Alasdair C.

    2000-01-01

    Poliovirus initiates infection by binding to its cellular receptor (Pvr). We have studied this interaction by using cryoelectron microscopy to determine the structure, at 21-Å resolution, of poliovirus complexed with a soluble form of its receptor (sPvr). This density map aided construction of a homology-based model of sPvr and, in conjunction with the known crystal structure of the virus, allowed delineation of the binding site. The virion does not change significantly in structure on binding sPvr in short incubations at 4°C. We infer that the binding configuration visualized represents the initial interaction that is followed by structural changes in the virion as infection proceeds. sPvr is segmented into three well-defined Ig-like domains. The two domains closest to the virion (domains 1 and 2) are aligned and rigidly connected, whereas domain 3 diverges at an angle of ≈60°. Two nodules of density on domain 2 are identified as glycosylation sites. Domain 1 penetrates the “canyon” that surrounds the 5-fold protrusion on the capsid surface, and its binding site involves all three major capsid proteins. The inferred pattern of virus–sPvr interactions accounts for most mutations that affect the binding of Pvr to poliovirus. PMID:10618373

  1. Method and apparatus for evaluating structural weakness in polymer matrix composites

    Science.gov (United States)

    Wachter, Eric A.; Fisher, Walter G.

    1996-01-01

    A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image.

  2. Characterization and reactivity of the weakly bound complexes of the [H, N, S]{sup −} anionic system with astrophysical and biological implications

    Energy Technology Data Exchange (ETDEWEB)

    Trabelsi, T.; Ajili, Y.; Ben Yaghlane, S.; Jaidane, N.-E. [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications–LSAMA, Université de Tunis El Manar, Tunis (Tunisia); Mogren Al-Mogren, M. [Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Francisco, J. S. [Department of Chemistry and Department of Earth and Atmospheric Sciences, Purdue University, West Lafayette, Indiana 47906 (United States); Hochlaf, M., E-mail: hochlaf@univ-mlv.fr [Laboratoire Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, 5 Blvd. Descartes, 77454 Marne-la-Vallée (France)

    2015-07-21

    We investigate the lowest electronic states of doublet and quartet spin multiplicity states of HNS{sup −} and HSN{sup −} together with their parent neutral triatomic molecules. Computations were performed using highly accurate ab initio methods with a large basis set. One-dimensional cuts of the full-dimensional potential energy surfaces (PESs) along the interatomic distances and bending angle are presented for each isomer. Results show that the ground anionic states are stable with respect to the electron detachment process and that the long range parts of the PESs correlating to the SH{sup −} + N, SN{sup −} + H, SN + H{sup −}, NH + S{sup −}, and NH{sup −} + S are bound. In addition, we predict the existence of long-lived weakly bound anionic complexes that can be formed after cold collisions between SN{sup −} and H or SH{sup −} and N. The implications for the reactivity of these species are discussed; specifically, it is shown that the reactions involving SH{sup −}, SN{sup −}, and NH{sup −} lead either to the formation of HNS{sup −} or HSN{sup −} in their electronic ground states or to autodetachment processes. Thus, providing an explanation for why the anions, SH{sup −}, SN{sup −}, and NH{sup −}, have limiting detectability in astrophysical media despite the observation of their corresponding neutral species. In a biological context, we suggest that HSN{sup −} and HNS{sup −} should be incorporated into H{sub 2}S-assisted heme-catalyzed reduction mechanism of nitrites in vivo.

  3. Crystal structure of rofecoxib bound to human cyclooxygenase-2

    Energy Technology Data Exchange (ETDEWEB)

    Orlando, Benjamin J.; Malkowski, Michael G. (Buffalo)

    2016-10-26

    Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization conditions were identified that allowed the structural determination of human COX-2 in complex with Vioxx and the structure was subsequently determined to 2.7- Å resolution. The crystal structure provides the first atomic level details of the binding of Vioxx to COX-2. As anticipated, Vioxx binds with its methyl sulfone moiety located in the side pocket of the cyclooxygenase channel, providing support for the isoform selectivity of this drug.

  4. Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome.

    Science.gov (United States)

    Li, Xiaojun; Sun, Qingan; Jiang, Cai; Yang, Kailu; Hung, Li-Wei; Zhang, Junjie; Sacchettini, James C

    2015-10-06

    The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Crystal Structure of an LSD-Bound Human Serotonin Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D.; Betz, Robin M.; Venkatakrishnan, A.J.; Levit, Anat; Lansu, Katherine; Schools, Zachary L.; Che, Tao; Nichols, David E.; Shoichet, Brian K.; Dror, Ron O.; Roth, Bryan L. (UNCSM); (UNC); (Stanford); (Stanford-MED); (UCSF)

    2017-01-01

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.

  6. Crystal Structure of an LSD-Bound Human Serotonin Receptor.

    Science.gov (United States)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D; Betz, Robin M; Venkatakrishnan, A J; Levit, Anat; Lansu, Katherine; Schools, Zachary L; Che, Tao; Nichols, David E; Shoichet, Brian K; Dror, Ron O; Roth, Bryan L

    2017-01-26

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Preliminary Results on the Experimental Investigation of the Structure Functions of Bound Nucleons

    Energy Technology Data Exchange (ETDEWEB)

    Bodek, Arie [Univ. of Rochester, NY (United States); Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2016-08-01

    We present preliminary results on an experimental study of the nuclear modification of the longitudinal ($\\sigma_L$) and transverse ($\\sigma_T$) structure functions of nucleons bound in nuclear targets. The origin of these modifications (commonly referred as as the EMC effect) is not fully understood. Our measurements of R= $\\sigma_L / \\sigma_T$ for nuclei ($R_A$) and for deuterium ($R_D$) indicate that nuclear modifications of the structure functions of bound nucleons are different for the longitudinal and transverse structure functions, and that contrary to expectation from several theoretical models, $R_A< R_D$.

  8. Structures of Potent Selective Peptide Mimetics Bound to Carboxypeptidase B

    Energy Technology Data Exchange (ETDEWEB)

    Adler, M.; Buckman, B.; Bryant, J.; Chang, Z.; Chu, K.; Emayan, K.; Hrvatin, P.; Islam, I.; Morser, J.; Sukovich, D.; West, C.; Yuan, S.; Whitlow, M.

    2009-05-11

    This article reports the crystal structures of inhibitors of the functional form of thrombin-activatable fibrinolysis inhibitor (TAFIa). In vivo experiments indicate that selective inhibitors of TAFIa would be useful in the treatment of heart attacks. Since TAFIa rapidly degrades in solution, the homologous protein porcine pancreatic carboxypeptidase B (pp-CpB) was used in these crystallography studies. Both TAFIa and pp-CpB are zinc-based exopeptidases that are specific for basic residues. The final development candidate, BX 528, is a potent inhibitor of TAFIa (2 nM) and has almost no measurable effect on the major selectivity target, carboxypeptidase N. BX 528 was designed to mimic the tripeptide Phe-Val-Lys. A sulfonamide replaces the Phe-Val amide bond and a phosphinate connects the Val and Lys groups. The phosphinate also chelates the active-site zinc. The electrostatic interactions with the protein mimic those of the natural substrate. The primary amine in BX 528 forms a salt bridge to Asp255 at the base of the S1 pocket. The carboxylic acid interacts with Arg145 and the sulfonamide is hydrogen bonded to Arg71. Isopropyl and phenyl groups replace the side chains of Val and Phe, respectively. A series of structures are presented here that illustrate the evolution of BX 528 from thiol-based inhibitors that mimic a free C-terminal arginine. The first step in development was the replacement of the thiol with a phosphinate. This caused a precipitous drop in binding affinity. Potency was reclaimed by extending the inhibitors into the downstream binding sites for the natural substrate.

  9. Long clinostation influence on the localization of free and weakly bound calcium in cell walls of Funaria hygrometrica moss protonema cells

    Science.gov (United States)

    Nedukha, E. M.

    The pyroantimonate method was used to study the localization of free and weakly bound calcium in cells of moss protonema of Funaria hygrometrica Hedw. cultivated on a clinostat (2 rev/min). Electroncytochemical study of control cells cultivated at 1 g revealed that granular precipitate marked chloroplasts, mitochondria, Golgi apparatus, lipid drops, nucleoplasma, nucleolus, nucleus membranes, cell walls and endoplasmic reticulum. In mitochondria the precipitate was revealed in stroma, in chloroplast it was found on thylakoids and envelope membranes. The cultivation of protonema on clinostat led to the intensification in cytochemical reaction product deposit. A considerable intensification of the reaction was noted in endomembranes, vacuoles, periplasmic space and cell walls. At the same time analysis of pectinase localization was made using the electroncytochemical method. A high reaction intensity in walls in comparison to that in control was found out to be a distinctive pecularity of the cells cultivated on clinostat. It testifies to the fact that increasing of freee calcium concentrations under conditions of clinostation is connected with pectinic substances hydrolysis and breaking of methoxy groups of pectins. Data obtained are discussed in relation to problems of possible mechanisms of disturbance in calcium balance of plant cells and the role of cell walls in gomeostasis of cell grown under conditions of simulated weighlessness.

  10. SFG analysis of surface bound proteins: a route towards structure determination.

    Science.gov (United States)

    Weidner, Tobias; Castner, David G

    2013-08-14

    The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

  11. Structure of RNA 3'-phosphate cyclase bound to substrate RNA.

    Science.gov (United States)

    Desai, Kevin K; Bingman, Craig A; Cheng, Chin L; Phillips, George N; Raines, Ronald T

    2014-10-01

    RNA 3'-phosphate cyclase (RtcA) catalyzes the ATP-dependent cyclization of a 3'-phosphate to form a 2',3'-cyclic phosphate at RNA termini. Cyclization proceeds through RtcA-AMP and RNA(3')pp(5')A covalent intermediates, which are analogous to intermediates formed during catalysis by the tRNA ligase RtcB. Here we present a crystal structure of Pyrococcus horikoshii RtcA in complex with a 3'-phosphate terminated RNA and adenosine in the AMP-binding pocket. Our data reveal that RtcA recognizes substrate RNA by ensuring that the terminal 3'-phosphate makes a large contribution to RNA binding. Furthermore, the RNA 3'-phosphate is poised for in-line attack on the P-N bond that links the phosphorous atom of AMP to N(ε) of His307. Thus, we provide the first insights into RNA 3'-phosphate termini recognition and the mechanism of 3'-phosphate activation by an Rtc enzyme. © 2014 Desai et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  12. Size and Structure of Cytochrome-c bound to Gold nano-clusters ...

    Indian Academy of Sciences (India)

    Size and structure of cytochrome c (Cyt C) bound to gold nano-clusters (AuNC) were studied using fluorescence correlation spectroscopy (FCS) and circular dichroism (CD) spectroscopy. The CD spectra of Cyt C indicate that the ellipticity is almost completely lost on binding to AuNC which indicates unfolding.Addition of ...

  13. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

    DEFF Research Database (Denmark)

    Link, Todd M; Valentin-Hansen, Poul; Brennan, Richard G

    2009-01-01

    studies. Indeed, Hfq bound to the oligoribonucleotides (AGG)(8), (AGC)(8), and the shorter (A-R-N)(4) sequence, AACAACAAGAAG, with nanomolar affinities. The abundance of (A-R-N)(4) and (A-R-N)(5) triplet repeats in the E. coli genome suggests additional RNA targets for Hfq. Further, the structure provides...

  14. Algorithms for singularities and real structures of weak Del Pezzo surfaces

    KAUST Repository

    Lubbes, Niels

    2014-08-01

    In this paper, we consider the classification of singularities [P. Du Val, On isolated singularities of surfaces which do not affect the conditions of adjunction. I, II, III, Proc. Camb. Philos. Soc. 30 (1934) 453-491] and real structures [C. T. C. Wall, Real forms of smooth del Pezzo surfaces, J. Reine Angew. Math. 1987(375/376) (1987) 47-66, ISSN 0075-4102] of weak Del Pezzo surfaces from an algorithmic point of view. It is well-known that the singularities of weak Del Pezzo surfaces correspond to root subsystems. We present an algorithm which computes the classification of these root subsystems. We represent equivalence classes of root subsystems by unique labels. These labels allow us to construct examples of weak Del Pezzo surfaces with the corresponding singularity configuration. Equivalence classes of real structures of weak Del Pezzo surfaces are also represented by root subsystems. We present an algorithm which computes the classification of real structures. This leads to an alternative proof of the known classification for Del Pezzo surfaces and extends this classification to singular weak Del Pezzo surfaces. As an application we classify families of real conics on cyclides. © World Scientific Publishing Company.

  15. Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.

    Science.gov (United States)

    Li, Jun; Dantas Machado, Ana Carolina; Guo, Ming; Sagendorf, Jared M; Zhou, Zhan; Jiang, Longying; Chen, Xiaojuan; Wu, Daichao; Qu, Lingzhi; Chen, Zhuchu; Chen, Lin; Rohs, Remo; Chen, Yongheng

    2017-07-25

    FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). The FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry assays suggested that this region was required for optimal DNA binding. Structure comparison with the FOXA3-DBD bound to DNA revealed more major groove contacts and fewer minor groove contacts in the FOXA2 structure than in the FOXA3 structure. Structure comparison with the FOXO1-DBD bound to DNA showed that different forkhead proteins could induce different DNA conformations upon binding to identical DNA sequences. Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites.

  16. Partially persistent data structures of bounded degree with constant update time

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting

    1996-01-01

    The problem of making bounded in-degree and out-degree data structures partially persistent is considered. The node copying method of Driscoll et al. is extended so that updates can be performed in worst-case constant time on the pointer machine model. Previously it was only known to be possible...... in amortised constant time.The result is presented in terms of a new strategy for Dietz and Raman's dynamic two player pebble game on graphs.It is shown how to implement the strategy and the upper bound on the required number of pebbles is improved from 2b+2d+O(√b) to d+2b. where b is the bound of the in...

  17. Structure and orientation of dynorphin bound to lipid bilayers by 13C solid-state NMR

    Science.gov (United States)

    Uezono, Takiko; Toraya, Shuichi; Obata, Maki; Nishimura, Katsuyuki; Tuzi, Satoru; Saitô, Hazime; Naito, Akira

    2005-07-01

    Secondary structure and orientation of dynorphin bound to dimyristoylphosphatidylcholine (DMPC) bilayer were investigated by solid-state 13C NMR spectroscopy. For this purpose, 13C NMR spectra of the site-specifically 13C-labeled dynorphin were measured in the membrane-bound state under static, magic angle spinning (MAS), and slow MAS conditions. In the static experiment, magnetically oriented vesicle system (MOVS) induced by dynorphin was successfully used to investigate the orientation of dynorphin bound to the lipid bilayers. It was found that dynorphin adopts an α-helical structure in the N-terminus from Gly 2 to Leu 5 by analyses of the isotropic chemical shifts obtained from the MAS experiments. In contrast, it adopts disordered conformations from the center to the C-terminus and is located on the membrane surface. The static 13C NMR spectra indicated that MOVS-bound dynorphin was oriented to the magnetic field and rotated rapidly about the bilayer normal. Subsequently, we analyzed the 13C chemical shift tensors of carbonyl carbons in the peptide backbone by considering the rotational motion of the N-terminal α-helix. It was revealed that the N-terminal α-helix is inserted into the membrane with the tilt angle of 21° to the bilayer normal. This structure suggests a possibility that dynorphin interacts with the extracellular loop II of the κ-receptor through a helix-helix interaction.

  18. Stability strengths and weaknesses in protein structures detected by statistical potentials: Application to bovine seminal ribonuclease.

    Science.gov (United States)

    De Laet, Marie; Gilis, Dimitri; Rooman, Marianne

    2016-01-01

    We present an in silico method to estimate the contribution of each residue in a protein to its overall stability using three database-derived statistical potentials that are based on inter-residue distances, backbone torsion angles and solvent accessibility, respectively. Residues that contribute very unfavorably to the folding free energy are defined as stability weaknesses, whereas residues that show a highly stabilizing contribution are called stability strengths. Strengths and/or weaknesses on residues that are in spatial contact are clustered into 3-dimensional (3D) stability patches. The identification and analysis of strength- and weakness-containing regions in a protein may reveal structural or functional characteristics, and/or interesting spots to introduce mutations. To illustrate the power of our method, we apply it to bovine seminal ribonuclease. This enzyme catalyzes the degradation of RNA strands, and has the peculiarity of undergoing 3D domain swapping in physiological conditions. The weaknesses and strengths were compared among the monomeric, dimeric and swapped dimeric forms. We identified weaknesses among the catalytic residues and a mixture of weaknesses and strengths among the substrate-binding residues in the three forms. In the regions involved in 3D swapping, we observed an accumulation of weaknesses in the monomer, which disappear in the dimer and especially in the swapped dimer. Moreover, monomeric homologous proteins were found to exhibit less weaknesses in these regions, whereas mutants known to favor unswapped dimerization appear stabilized in this form. Our method has several perspectives for functional annotation, rational prediction of targeted mutations, and mapping of stability changes upon conformational rearrangements. © 2015 Wiley Periodicals, Inc.

  19. Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP.

    Directory of Open Access Journals (Sweden)

    Kap Lim

    Full Text Available The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP, was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123-170, which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent.

  20. Structured Uncertainty Bound Determination From Data for Control and Performance Validation

    Science.gov (United States)

    Lim, Kyong B.

    2003-01-01

    This report attempts to document the broad scope of issues that must be satisfactorily resolved before one can expect to methodically obtain, with a reasonable confidence, a near-optimal robust closed loop performance in physical applications. These include elements of signal processing, noise identification, system identification, model validation, and uncertainty modeling. Based on a recently developed methodology involving a parameterization of all model validating uncertainty sets for a given linear fractional transformation (LFT) structure and noise allowance, a new software, Uncertainty Bound Identification (UBID) toolbox, which conveniently executes model validation tests and determine uncertainty bounds from data, has been designed and is currently available. This toolbox also serves to benchmark the current state-of-the-art in uncertainty bound determination and in turn facilitate benchmarking of robust control technology. To help clarify the methodology and use of the new software, two tutorial examples are provided. The first involves the uncertainty characterization of a flexible structure dynamics, and the second example involves a closed loop performance validation of a ducted fan based on an uncertainty bound from data. These examples, along with other simulation and experimental results, also help describe the many factors and assumptions that determine the degree of success in applying robust control theory to practical problems.

  1. Crystal Structure of NFAT Bound to the HIV-1 LTR Tandem κB Enhancer Element

    Energy Technology Data Exchange (ETDEWEB)

    Bates, Darren L.; Barthel, Kristen K.B.; Wu, Yongqing; Kalhor, Reza; Stroud, James C.; Giffin, Michael J.; Chen, Lin (UCLA); (Colorado)

    2008-05-27

    Here, we have determined the crystal structure of the DNA binding domain of NFAT bound to the HIV-1 long terminal repeat (LTR) tandem {kappa}B enhancer element of 3.05 {angstrom} resolution. NFAT binds as a dimer to the upstream {kappa}B site (Core II), but as a monomer to the 3' end of the downstream {kappa}B site (Core I). The DNA shows a significant bend near the 5' end of Core I, where a lysine residue from NFAT bound to the 3' end of Core II inserts into the minor groove and seems to cause DNA bases to flip out. Consistent with this structural feature, the 5' end of Core I become hypersensitive to dimethylsulfate in the in vivo footprinting upon transcriptional activation of the HIV-1 LTR. Our studies provide a basis for futher investigating the functional mechanism of NFAT in HIV-1 transcription and replication.

  2. Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.

    Science.gov (United States)

    Thompson, Michael C; Crowley, Christopher S; Kopstein, Jeffrey; Bobik, Thomas A; Yeates, Todd O

    2014-12-01

    The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein-ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.

  3. Molecular characterization of structural genes coding for a membrane bound hydrogenase in Methylococcus capsulatus (Bath).

    Science.gov (United States)

    Csáki, R; Hanczár, T; Bodrossy, L; Murrell, J C; Kovács, K L

    2001-12-18

    The first gene cluster encoding for a membrane bound [NiFe] hydrogenase from a methanotroph, Methylococcus capsulatus (Bath), was cloned and sequenced. The cluster consisted of the structural genes hupS and hupL and accessory genes hupE, hupC and hupD. A DeltahupSL deletion mutant of Mc. capsulatus was constructed by marker exchange mutagenesis. Membrane associated hydrogenase activity disappeared. The membrane associated hydrogenase appeared to have a hydrogen uptake function in vivo.

  4. P 6- and triangle-free graphs revisited: structure and bounded clique-width

    Directory of Open Access Journals (Sweden)

    Andreas Brandstädt

    2006-01-01

    Full Text Available The Maximum Weight Stable Set (MWS Problem is one of the fundamental problems on graphs. It is well-known to be NP-complete for triangle-free graphs, and Mosca has shown that it is solvable in polynomial time when restricted to P 6- and triangle-free graphs. We give a complete structure analysis of (nonbipartite P 6- and triangle-free graphs which are prime in the sense of modular decomposition. It turns out that the structure of these graphs is extremely simple implying bounded clique-width and thus, efficient algorithms exist for all problems expressible in terms of Monadic Second Order Logic with quantification only over vertex predicates. The problems Vertex Cover, MWS, Maximum Clique, Minimum Dominating Set, Steiner Tree, and Maximum Induced Matching are among them. Our results improve the previous one on the MWS problem by Mosca with respect to structure and time bound but also extends a previous result by Fouquet, Giakoumakis and Vanherpe which have shown that bipartite P 6-free graphs have bounded clique-width. Moreover, it covers a result by Randerath, Schiermeyer and Tewes on polynomial time 3-colorability of P 6- and triangle-free graphs.

  5. Crystal Structure of Inhibitor-Bound P450BM-3 Reveals Open Conformation of Substrate Access Channel

    Energy Technology Data Exchange (ETDEWEB)

    Haines, Donovan C.; Chen, Baozhi; Tomchick, Diana R.; Bondlela, Muralidhar; Hegde, Amita; Machius, Mischa; Peterson, Julian A. (Texas); (UTSMC)

    2008-08-19

    P450BM-3 is an extensively studied P450 cytochrome that is naturally fused to a cytochrome P450 reductase domain. Crystal structures of the heme domain of this enzyme have previously generated many insights into features of P450 structure, substrate binding specificity, and conformational changes that occur on substrate binding. Although many P450s are inhibited by imidazole, this compound does not effectively inhibit P450BM-3. {omega}-Imidazolyl fatty acids have previously been found to be weak inhibitors of the enzyme and show some unusual cooperativity with the substrate lauric acid. We set out to improve the properties of these inhibitors by attaching the {omega}-imidazolyl fatty acid to the nitrogen of an amino acid group, a tactic that we used previously to increase the potency of substrates. The resulting inhibitors were significantly more potent than their parent compounds lacking the amino acid group. A crystal structure of one of the new inhibitors bound to the heme domain of P450BM-3 reveals that the mode of interaction of the amino acid group with the enzyme is different from that previously observed for acyl amino acid substrates. Further, required movements of residues in the active site to accommodate the imidazole group provide an explanation for the low affinity of imidazole itself. Finally, the previously observed cooperativity with lauric acid is explained by a surprisingly open substrate-access channel lined with hydrophobic residues that could potentially accommodate lauric acid in addition to the inhibitor itself.

  6. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA.

    Science.gov (United States)

    Liu, Yijin; Freeman, Alasdair D J; Déclais, Anne-Cécile; Wilson, Timothy J; Gartner, Anton; Lilley, David M J

    2015-12-22

    We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    Directory of Open Access Journals (Sweden)

    Yijin Liu

    2015-12-01

    Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

  8. Effect of substrate on optical bound states in the continuum in 1D photonic structures

    Science.gov (United States)

    Sadrieva, Z. F.; Sinev, I. S.; Samusev, A. K.; Iorsh, I. V.; Koshelev, K. L.; Takayama, O.; Malureanu, R.; Lavrinenko, A. V.; Bogdanov, A. A.

    2017-09-01

    Optical bound states in the continuum (BIC) are localized states with energy lying above the light line and having infinite lifetime. Any losses taking place in real systems result in transformation of the bound states into resonant states with finite lifetime. In this work, we analyze properties of BIC in CMOS-compatible one-dimensional photonic structure based on silicon-on-insulator wafer at telecommunication wavelengths, where the absorption of silicon is negligible. We reveal that a high-index substrate could destroy both off-Γ BIC and in-plane symmetry protected at-Γ BIC turning them into resonant states due to leakage into the diffraction channels opening in the substrate.

  9. Classical integrability for three-point functions: cognate structure at weak and strong couplings

    Energy Technology Data Exchange (ETDEWEB)

    Kazama, Yoichi [Research Center for Mathematical Physics, Rikkyo University,Toshima-ku, Tokyo 171-8501 (Japan); Quantum Hadron Physics Laboratory, RIKEN Nishina Center, Wako 351-0198 (Japan); Institute of Physics, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Komatsu, Shota [Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo, Ontario, N2L 2Y5 (Canada); Nishimura, Takuya [Institute of Physics, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2016-10-10

    In this paper, we develop a new method of computing three-point functions in the SU(2) sector of the N=4 super Yang-Mills theory in the semi-classical regime at weak coupling, which closely parallels the strong coupling analysis. The structure threading two disparate regimes is the so-called monodromy relation, an identity connecting the three-point functions with and without the insertion of the monodromy matrix. We shall show that this relation can be put to use directly for the semi-classical regime, where the dynamics is governed by the classical Landau-Lifshitz sigma model. Specifically, it reduces the problem to a set of functional equations, which can be solved once the analyticity in the spectral parameter space is specified. To determine the analyticity, we develop a new universal logic applicable at both weak and strong couplings. As a result, compact semi-classical formulas are obtained for a general class of three-point functions at weak coupling including the ones whose semi-classical behaviors were not known before. In addition, the new analyticity argument applied to the strong coupling analysis leads to a modification of the integration contour, producing the results consistent with the recent hexagon bootstrap approach. This modification also makes the Frolov-Tseytlin limit perfectly agree with the weak coupling form.

  10. Structural features and dynamic investigations of the membrane-bound cytochrome P450 17A1.

    Science.gov (United States)

    Cui, Ying-Lu; Xue, Qiao; Zheng, Qing-Chuan; Zhang, Ji-Long; Kong, Chui-Peng; Fan, Jing-Rong; Zhang, Hong-Xing

    2015-10-01

    Cytochrome P450 (CYP) 17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones. The enzyme is an important target for treatment of breast and prostate cancers that proliferate in response to estrogens and androgens. Despite the crystallographic structures available for CYP17A1, no membrane-bound structural features of this enzyme at atomic level are available. Accumulating evidence has indicated that the interactions between bounded CYPs and membrane could contribute to the recruitment of lipophilic substrates. To this end, we have investigated the effects on structural characteristics in the presence of the membrane for CYP17A1. The MD simulation results demonstrate a spontaneous insertion process of the enzyme to the lipid. Two predominant modes of CYP17A1 in the membrane are captured, characterized by the depths of insertion and orientations of the enzyme to the membrane surface. The measured heme tilt angles show good consistence with experimental data, thereby verifying the validity of the structural models. Moreover, conformational changes induced by the membrane might have impact on the accessibility of the active site to lipophilic substrates. The dynamics of internal aromatic gate formed by Trp220 and Phe224 are suggested to regulate tunnel opening motions. The knowledge of the membrane binding characteristics could guide future experimental and computational works on membrane-bound CYPs so that various investigations of CYPs in their natural, lipid environment rather than in artificially solubilized forms may be achieved. Copyright © 2015. Published by Elsevier B.V.

  11. Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Haga, Kazuko; Kruse, Andrew C.; Asada, Hidetsugu; Yurugi-Kobayashi, Takami; Shiroishi, Mitsunori; Zhang, Cheng; Weis, William I.; Okada, Tetsuji; Kobilka, Brian K.; Haga, Tatsuya; Kobayashi, Takuya (Stanford-MED); (Kyoto); (Gakushuin); (Kyushu)

    2012-03-15

    The parasympathetic branch of the autonomic nervous system regulates the activity of multiple organ systems. Muscarinic receptors are G-protein-coupled receptors that mediate the response to acetylcholine released from parasympathetic nerves. Their role in the unconscious regulation of organ and central nervous system function makes them potential therapeutic targets for a broad spectrum of diseases. The M2 muscarinic acetylcholine receptor (M2 receptor) is essential for the physiological control of cardiovascular function through activation of G-protein-coupled inwardly rectifying potassium channels, and is of particular interest because of its extensive pharmacological characterization with both orthosteric and allosteric ligands. Here we report the structure of the antagonist-bound human M2 receptor, the first human acetylcholine receptor to be characterized structurally, to our knowledge. The antagonist 3-quinuclidinyl-benzilate binds in the middle of a long aqueous channel extending approximately two-thirds through the membrane. The orthosteric binding pocket is formed by amino acids that are identical in all five muscarinic receptor subtypes, and shares structural homology with other functionally unrelated acetylcholine binding proteins from different species. A layer of tyrosine residues forms an aromatic cap restricting dissociation of the bound ligand. A binding site for allosteric ligands has been mapped to residues at the entrance to the binding pocket near this aromatic cap. The structure of the M2 receptor provides insights into the challenges of developing subtype-selective ligands for muscarinic receptors and their propensity for allosteric regulation.

  12. Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Hideshi, E-mail: h-yokoya@u-shizuoka-ken.ac.jp [School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 (Japan); Tsuruta, Osamu; Akao, Naoya; Fujii, Satoshi [School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 (Japan)

    2012-06-15

    Highlights: Black-Right-Pointing-Pointer Structures of a metal-bound Helicobacter pylori neutrophil-activating protein were determined. Black-Right-Pointing-Pointer Two zinc ions were tetrahedrally coordinated by ferroxidase center (FOC) residues. Black-Right-Pointing-Pointer Two cadmium ions were coordinated in a trigonal-bipyramidal and octahedral manner. Black-Right-Pointing-Pointer The second metal ion was more weakly coordinated than the first at the FOC. Black-Right-Pointing-Pointer A zinc ion was found in one negatively-charged pore suitable as an ion path. -- Abstract: Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn{sup 2+}- or Cd{sup 2+}-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.

  13. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    Science.gov (United States)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-01

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  14. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers.

    Science.gov (United States)

    Nap, R J; Tagliazucchi, M; Szleifer, I

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  15. Resolving the Spatial Structures of Bound Hole States in Black Phosphorus.

    Science.gov (United States)

    Qiu, Zhizhan; Fang, Hanyan; Carvalho, Alexandra; Rodin, A S; Liu, Yanpeng; Tan, Sherman J R; Telychko, Mykola; Lv, Pin; Su, Jie; Wang, Yewu; Castro Neto, A H; Lu, Jiong

    2017-11-08

    Understanding the local electronic properties of individual defects and dopants in black phosphorus (BP) is of great importance for both fundamental research and technological applications. Here, we employ low-temperature scanning tunnelling microscope (LT-STM) to probe the local electronic structures of single acceptors in BP. We demonstrate that the charge state of individual acceptors can be reversibly switched by controlling the tip-induced band bending. In addition, acceptor-related resonance features in the tunnelling spectra can be attributed to the formation of Rydberg-like bound hole states. The spatial mapping of the quantum bound states shows two distinct shapes evolving from an extended ellipse shape for the 1s ground state to a dumbbell shape for the 2p x excited state. The wave functions of bound hole states can be well-described using the hydrogen-like model with anisotropic effective mass, corroborated by our theoretical calculations. Our findings not only provide new insight into the many-body interactions around single dopants in this anisotropic two-dimensional material but also pave the way to the design of novel quantum devices.

  16. Crystal structures of agonist-bound human cannabinoid receptor CB1.

    Science.gov (United States)

    Hua, Tian; Vemuri, Kiran; Nikas, Spyros P; Laprairie, Robert B; Wu, Yiran; Qu, Lu; Pu, Mengchen; Korde, Anisha; Jiang, Shan; Ho, Jo-Hao; Han, Gye Won; Ding, Kang; Li, Xuanxuan; Liu, Haiguang; Hanson, Michael A; Zhao, Suwen; Bohn, Laura M; Makriyannis, Alexandros; Stevens, Raymond C; Liu, Zhi-Jie

    2017-07-27

    The cannabinoid receptor 1 (CB1) is the principal target of the psychoactive constituent of marijuana, the partial agonist Δ(9)-tetrahydrocannabinol (Δ(9)-THC). Here we report two agonist-bound crystal structures of human CB1 in complex with a tetrahydrocannabinol (AM11542) and a hexahydrocannabinol (AM841) at 2.80 Å and 2.95 Å resolution, respectively. The two CB1-agonist complexes reveal important conformational changes in the overall structure, relative to the antagonist-bound state, including a 53% reduction in the volume of the ligand-binding pocket and an increase in the surface area of the G-protein-binding region. In addition, a 'twin toggle switch' of Phe200(3.36) and Trp356(6.48) (superscripts denote Ballesteros-Weinstein numbering) is experimentally observed and appears to be essential for receptor activation. The structures reveal important insights into the activation mechanism of CB1 and provide a molecular basis for predicting the binding modes of Δ(9)-THC, and endogenous and synthetic cannabinoids. The plasticity of the binding pocket of CB1 seems to be a common feature among certain class A G-protein-coupled receptors. These findings should inspire the design of chemically diverse ligands with distinct pharmacological properties.

  17. Structure and function of emergency care research networks: strengths, weaknesses, and challenges.

    Science.gov (United States)

    Papa, Linda; Kuppermann, Nathan; Lamond, Katherine; Barsan, William G; Camargo, Carlos A; Ornato, Joseph P; Stiell, Ian G; Talan, David A

    2009-10-01

    The ability of emergency care research (ECR) to produce meaningful improvements in the outcomes of acutely ill or injured patients depends on the optimal configuration, infrastructure, organization, and support of emergency care research networks (ECRNs). Through the experiences of existing ECRNs, we can learn how to best accomplish this. A meeting was organized in Washington, DC, on May 28, 2008, to discuss the present state and future directions of clinical research networks as they relate to emergency care. Prior to the conference, at the time of online registration, participants responded to a series of preconference questions addressing the relevant issues that would form the basis of the breakout session discussions. During the conference, representatives from a number of existing ECRNs participated in discussions with the attendees and provided a description of their respective networks, infrastructure, and challenges. Breakout sessions provided the opportunity to further discuss the strengths and weaknesses of these networks and patterns of success with respect to their formation, management, funding, best practices, and pitfalls. Discussions centered on identifying characteristics that promote or inhibit successful networks and their interactivity, productivity, and expansion. Here the authors describe the current state of ECRNs and identify the strengths, weaknesses, and potential pitfalls of research networks. The most commonly cited strengths of population- or disease-based research networks identified in the preconference survey were access to larger numbers of patients; involvement of physician experts in the field, contributing to high-level study content; and the collaboration among investigators. The most commonly cited weaknesses were studies with too narrow a focus and restrictive inclusion criteria, a vast organizational structure with a risk of either too much or too little central organization or control, and heterogeneity of institutional

  18. Effects of weak nonlinearity on dispersion relations and frequency band-gaps of periodic structures

    DEFF Research Database (Denmark)

    Sorokin, Vladislav; Thomsen, Jon Juel

    2015-01-01

    . Determination of band-gaps and the corresponding attenuation levels is an im-portant practical problem. Most existing analytical methods in the field are based on Floquet theory; e.g. this holds for the classical Hill’s method of infinite determinants, and the method of space-harmonics. However, application...... of these for nonlinear problems is impossible or cumbersome, since Floquet theory is applicable for linear systems only. Thus the nonlinear effects for periodic structures are not yet fully uncovered, while at the same time applica-tions may demand effects of nonlinearity on structural response to be accounted for....... The present work deals with analytically predicting dynamic responses for nonlinear continuous elastic periodic structures. Specifically, the effects of weak nonlinearity on the dispersion re-lation and frequency band-gaps of a periodic Bernoulli-Euler beam performing bending os-cillations are analyzed...

  19. Avalanche structural rearrangement through cracking-healing in weakly stressed cold dusty plasma liquids.

    Science.gov (United States)

    Yang, Chi; Wang, Wen; I, Lin

    2016-01-01

    We experimentally investigate the spatiotemporal dynamical behaviors of the avalanche structural rearrangement through micro-cracking-healing in weakly stressed cold dusty plasma liquids, and the kinetic origins for their different spatial and temporal classifications. The crystalline ordered domains can be cracked or temporarily sustain and transfer the weak stress to remote regions for cracking-healing. It is found that cracking sites form a fractal network with cluster size following power law distribution in the xyt space. The histograms of the persistent times for sustaining regional ordered and disordered structure, the temporal cracking burst width, and quiescent time between two bursts all follow power law decays with fast descending tails. Cracking can be classified into a single temporal burst with simple line like spatial patterns and the successive cracking fluctuation with densely packed cracking clusters. For an ordered region, whether the Burgers vectors of the incoming dislocations from the boundary allow direct dislocation reduction is the key for the above two classifications through cracking a large ordered domain into medium scale corotating ordered domains or small patches. The low regional structural order at the end of a cracking burst can be regarded as an alarm for predicting the short quiescent period before the next cracking burst.

  20. The thermal stability of the nanograin structure in a weak solute segregation system.

    Science.gov (United States)

    Tang, Fawei; Song, Xiaoyan; Wang, Haibin; Liu, Xuemei; Nie, Zuoren

    2017-02-08

    A hybrid model that combines first principles calculations and thermodynamic evaluation was developed to describe the thermal stability of a nanocrystalline solid solution with weak segregation. The dependence of the solute segregation behavior on the electronic structure, solute concentration, grain size and temperature was demonstrated, using the nanocrystalline Cu-Zn system as an example. The modeling results show that the segregation energy changes with the solute concentration in a form of nonmonotonic function. The change in the total Gibbs free energy indicates that at a constant solute concentration and a given temperature, a nanocrystalline structure can remain stable when the initial grain size is controlled in a critical range. In experiments, dense nanocrystalline Cu-Zn alloy bulk was prepared, and a series of annealing experiments were performed to examine the thermal stability of the nanograins. The experimental measurements confirmed the model predictions that with a certain solute concentration, a state of steady nanograin growth can be achieved at high temperatures when the initial grain size is controlled in a critical range. The present work proposes that in weak solute segregation systems, the nanograin structure can be kept thermally stable by adjusting the solute concentration and initial grain size.

  1. Aging population in change – a crucial challenge for structurally weak rural areas in Austria

    Directory of Open Access Journals (Sweden)

    Fischer Tatjana

    2014-03-01

    Full Text Available Besides population decline, structurally weak rural areas in Austria face a new challenge related to demographic change: the increasing heterogeneity of their aging population. From the example of the so-called ‘best agers’ - comprising people aged 55 to 65 years - this contribution makes visible patterns and consequences of growing individualized spatial behaviour and spatial perception. Furthermore, contradictions between claims, wishes and expectations and actual engagement and commitment to their residential rural municipalities are being pointed out. These empirically-based facts are rounded off by considerations on the best agers’ future migration-behaviour and the challenges for spatial planning at the municipal level.

  2. Revisiting the Structures of Several Antibiotics Bound to the Bacterial Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    D Bulkley; C Innis; G Blaha; T Steitz

    2011-12-31

    The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.

  3. Revisiting the structures of several antibiotics bound to the bacterial ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Bulkley, David; Innis, C. Axel; Blaha, Gregor; Steitz, Thomas A. (Yale)

    2010-10-08

    The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.

  4. Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans.

    Science.gov (United States)

    Chan, Sum; Giuroiu, Iulia; Chernishof, Irina; Sawaya, Michael R; Chiang, Janet; Gunsalus, Robert P; Arbing, Mark A; Perry, L Jeanne

    2010-03-01

    The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 A resolution and in the molybdate-bound conformation at 2.25 and 2.45 A resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed alpha/beta domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the 'Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins.

  5. Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans

    Science.gov (United States)

    Chan, Sum; Giuroiu, Iulia; Chernishof, Irina; Sawaya, Michael R.; Chiang, Janet; Gunsalus, Robert P.; Arbing, Mark A.; Perry, L. Jeanne

    2010-01-01

    The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apo­protein conformation at 1.95 and 1.69 Å resolution and in the molybdate-bound conformation at 2.25 and 2.45 Å resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed α/β domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the ‘Venus flytrap’ model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins. PMID:20208152

  6. The crystal structure of tryptophan hydroxylase with bound amino acid substrate

    DEFF Research Database (Denmark)

    Windahl, Michael Skovbo; Petersen, Charlotte Rode; Christensen, Hans Erik Mølager

    2008-01-01

    Tryptophan hydroxylase (TPH) is a mononuclear non-heme iron enzyme, which catalyzes the reaction between tryptophan, O2, and tetrahydrobiopterin (BH4) to produce 5-hydroxytryptophan and 4a-hydroxytetrahydrobiopterin. This is the first and rate-limiting step in the biosynthesis of the neurotransmi......Tryptophan hydroxylase (TPH) is a mononuclear non-heme iron enzyme, which catalyzes the reaction between tryptophan, O2, and tetrahydrobiopterin (BH4) to produce 5-hydroxytryptophan and 4a-hydroxytetrahydrobiopterin. This is the first and rate-limiting step in the biosynthesis...... of the neurotransmitter and hormone serotonin (5-hydroxytryptamine). We have determined the 1.9 Å resolution crystal structure of the catalytic domain (Δ1−100/Δ415−445) of chicken TPH isoform 1 (TPH1) in complex with the tryptophan substrate and an iron-bound imidazole. This is the first structure of any aromatic amino...... acid hydroxylase with bound natural amino acid substrate. The iron coordination can be described as distorted trigonal bipyramidal coordination with His273, His278, and Glu318 (partially bidentate) and one imidazole as ligands. The tryptophan stacks against Pro269 with a distance of 3.9 Å between...

  7. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gagnon, M. G.; Lin, J.; Bulkley, D.; Steitz, T. A.

    2014-08-08

    Elongation factor 4 (EF4/LepA) is a highly conserved guanosine triphosphatase translation factor. It was shown to promote back-translocation of tRNAs on posttranslocational ribosome complexes and to compete with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis. Here, we report a crystal structure of EF4–guanosine diphosphate bound to the Thermus thermophilus ribosome with a P-site tRNA at 2.9 angstroms resolution. The C-terminal domain of EF4 reaches into the peptidyl transferase center and interacts with the acceptor stem of the peptidyl-tRNA in the P site. The ribosome is in an unusual state of ratcheting with the 30S subunit rotated clockwise relative to the 50S subunit, resulting in a remodeled decoding center. The structure is consistent with EF4 functioning either as a back-translocase or a ribosome sequester.

  8. Structure of REV-ERBβ Ligand-binding Domain Bound to a Porphyrin Antagonist*

    Science.gov (United States)

    Matta-Camacho, Edna; Banerjee, Subhashis; Hughes, Travis S.; Solt, Laura A.; Wang, Yongjun; Burris, Thomas P.; Kojetin, Douglas J.

    2014-01-01

    REV-ERBα and REV-ERBβ are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors that play important roles in the regulation of circadian physiology, metabolism, and immune function. Although the REV-ERBs were originally characterized as orphan receptors, recent studies have demonstrated that they function as receptors for heme. Here, we demonstrate that cobalt protoporphyrin IX (CoPP) and zinc protoporphyrin IX (ZnPP) are ligands that bind directly to the REV-ERBs. However, instead of mimicking the agonist action of heme, CoPP and ZnPP function as antagonists of REV-ERB function. This was unexpected because the only distinction between these ligands is the metal ion that is coordinated. To understand the structural basis by which REV-ERBβ can differentiate between a porphyrin agonist and antagonist, we characterized the interaction between REV-ERBβ with heme, CoPP, and ZnPP using biochemical and structural approaches, including x-ray crystallography and NMR. The crystal structure of CoPP-bound REV-ERBβ indicates only minor conformational changes induced by CoPP compared with heme, including the porphyrin ring of CoPP, which adopts a planar conformation as opposed to the puckered conformation observed in the heme-bound REV-ERBβ crystal structure. Thus, subtle changes in the porphyrin metal center and ring conformation may influence the agonist versus antagonist action of porphyrins and when considered with other studies suggest that gas binding to the iron metal center heme may drive alterations in REV-ERB activity. PMID:24872411

  9. Sliding surface searching method for slopes containing a potential weak structural surface

    Directory of Open Access Journals (Sweden)

    Aijun Yao

    2014-06-01

    Full Text Available Weak structural surface is one of the key factors controlling the stability of slopes. The stability of rock slopes is in general concerned with set of discontinuities. However, in soft rocks, failure can occur along surfaces approaching to a circular failure surface. To better understand the position of potential sliding surface, a new method called simplex-finite stochastic tracking method is proposed. This method basically divides sliding surface into two parts: one is described by smooth curve obtained by random searching, the other one is polyline formed by the weak structural surface. Single or multiple sliding surfaces can be considered, and consequently several types of combined sliding surfaces can be simulated. The paper will adopt the arc-polyline to simulate potential sliding surface and analyze the searching process of sliding surface. Accordingly, software for slope stability analysis using this method was developed and applied in real cases. The results show that, using simplex-finite stochastic tracking method, it is possible to locate the position of a potential sliding surface in the slope.

  10. Recovery of Weak Factor Loadings When Adding the Mean Structure in Confirmatory Factor Analysis: A Simulation Study.

    Science.gov (United States)

    Ximénez, Carmen

    2015-01-01

    This article extends previous research on the recovery of weak factor loadings in confirmatory factor analysis (CFA) by exploring the effects of adding the mean structure. This issue has not been examined in previous research. This study is based on the framework of Yung and Bentler (1999) and aims to examine the conditions that affect the recovery of weak factor loadings when the model includes the mean structure, compared to analyzing the covariance structure alone. A simulation study was conducted in which several constraints were defined for one-, two-, and three-factor models. Results show that adding the mean structure improves the recovery of weak factor loadings and reduces the asymptotic variances for the factor loadings, particularly for the models with a smaller number of factors and a small sample size. Therefore, under certain circumstances, modeling the means should be seriously considered for covariance models containing weak factor loadings.

  11. Breakdown of a space charge limited regime of a sheath in a weakly collisional plasma bounded by walls with secondary electron emission.

    Science.gov (United States)

    Sydorenko, D; Kaganovich, I; Raitses, Y; Smolyakov, A

    2009-10-02

    A new regime of plasma-wall interaction is identified in particle-in-cell simulations of a hot plasma bounded by walls with secondary electron emission. Such a plasma has a strongly non-Maxwellian electron velocity distribution function and consists of bulk plasma electrons and beams of secondary electrons. In the new regime, the plasma sheath is not in a steady space charge limited state even though the secondary electron emission produced by the plasma bulk electrons is so intense that the corresponding partial emission coefficient exceeds unity. Instead, the plasma-sheath system performs relaxation oscillations by switching quasiperiodically between the space charge limited and non-space-charge limited states.

  12. Phosphorylation Regulates the Bound Structure of an Intrinsically Disordered Protein: The p53-TAZ2 Case.

    Directory of Open Access Journals (Sweden)

    Raúl Esteban Ithuralde

    Full Text Available Disordered regions and Intrinsically Disordered Proteins (IDPs are involved in critical cellular processes and may acquire a stable three-dimensional structure only upon binding to their partners. IDPs may follow a folding-after-binding process, known as induced folding, or a folding-before-binding process, known as conformational selection. The transcription factor p53 is involved in the regulation of cellular events that arise upon stress or DNA damage. The p53 domain structure is composed of an N-terminal transactivation domain (p53TAD, a DNA Binding Domain and a tetramerization domain. The activity of TAD is tightly regulated by interactions with cofactors, inhibitors and phosphorylation. To initiate transcription, p53TAD binds to the TAZ2 domain of CBP, a co-transcription factor, and undergoes a folding and binding process, as revealed by the recent NMR structure of the complex. The activity of p53 is regulated by phosphorylation at multiple sites on the TAD domain and recent studies have shown that modifications at three residues affect the binding towards TAZ2. However, we still do not know how these phosphorylations affect the structure of the bound state and, therefore, how they regulate the p53 function. In this work, we have used computational simulations to understand how phosphorylation affects the structure of the p53TAD:TAZ2 complex and regulates the recognition mechanism. Phosphorylation has been proposed to enhance binding by direct interaction with the folded protein or by changing the unbound conformation of IDPs, for example by pre-folding the protein favoring the recognition mechanism. Here, we show an interesting turn in the p53 case: phosphorylation mainly affects the bound structure of p53TAD, highlighting the complexity of IDP protein-protein interactions. Our results are in agreement with previous experimental studies, allowing a clear picture of how p53 is regulated by phosphorylation and giving new insights into how

  13. Structure and function of membrane proteins encapsulated in a polymer-bound lipid bilayer.

    Science.gov (United States)

    Pollock, Naomi L; Lee, Sarah C; Patel, Jaimin H; Gulamhussein, Aiman A; Rothnie, Alice J

    2018-04-01

    New technologies for the purification of stable membrane proteins have emerged in recent years, in particular methods that allow the preparation of membrane proteins with their native lipid environment. Here, we look at the progress achieved with the use of styrene-maleic acid copolymers (SMA) which are able to insert into biological membranes forming nanoparticles containing membrane proteins and lipids. This technology can be applied to membrane proteins from any host source, and, uniquely, allows purification without the protein ever being removed from a lipid bilayer. Not only do these SMA lipid particles (SMALPs) stabilise membrane proteins, allowing structural and functional studies, but they also offer opportunities to understand the local lipid environment of the host membrane. With any new or different method, questions inevitably arise about the integrity of the protein purified: does it retain its activity; its native structure; and ability to perform its function? How do membrane proteins within SMALPS perform in existing assays and lend themselves to analysis by established methods? We outline here recent work on the structure and function of membrane proteins that have been encapsulated like this in a polymer-bound lipid bilayer, and the potential for the future with this approach. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function

    Directory of Open Access Journals (Sweden)

    Michael W. Reimann

    2017-06-01

    Full Text Available The lack of a formal link between neural network structure and its emergent function has hampered our understanding of how the brain processes information. We have now come closer to describing such a link by taking the direction of synaptic transmission into account, constructing graphs of a network that reflect the direction of information flow, and analyzing these directed graphs using algebraic topology. Applying this approach to a local network of neurons in the neocortex revealed a remarkably intricate and previously unseen topology of synaptic connectivity. The synaptic network contains an abundance of cliques of neurons bound into cavities that guide the emergence of correlated activity. In response to stimuli, correlated activity binds synaptically connected neurons into functional cliques and cavities that evolve in a stereotypical sequence toward peak complexity. We propose that the brain processes stimuli by forming increasingly complex functional cliques and cavities.

  15. Finite Elements Based on Strong and Weak Formulations for Structural Mechanics: Stability, Accuracy and Reliability

    Directory of Open Access Journals (Sweden)

    Francesco Tornabene

    2017-07-01

    Full Text Available The authors are presenting a novel formulation based on the Differential Quadrature (DQ method which is used to approximate derivatives and integrals. The resulting scheme has been termed strong and weak form finite elements (SFEM or WFEM, according to the numerical scheme employed in the computation. Such numerical methods are applied to solve some structural problems related to the mechanical behavior of plates and shells, made of isotropic or composite materials. The main differences between these two approaches rely on the initial formulation – which is strong or weak (variational – and the implementation of the boundary conditions, that for the former include the continuity of stresses and displacements, whereas in the latter can consider the continuity of the displacements or both. The two methodologies consider also a mapping technique to transform an element of general shape described in Cartesian coordinates into the same element in the computational space. Such technique can be implemented by employing the classic Lagrangian-shaped elements with a fixed number of nodes along the element edges or blending functions which allow an “exact mapping” of the element. In particular, the authors are employing NURBS (Not-Uniform Rational B-Splines for such nonlinear mapping in order to use the “exact” shape of CAD designs.

  16. Weak links between fast mobility and local structure in molecular and atomic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Bernini, S. [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Puosi, F. [Laboratoire de Physique de l’École Normale Supérieure de Lyon, UMR CNRS 5672, 46 allée d’Italie, 69007 Lyon (France); Leporini, D., E-mail: dino.leporini@df.unipi.it [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); IPCF-CNR, UOS Pisa, Pisa (Italy)

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  17. Molecular cloning, characterisation and ligand-bound structure of an azoreductase from Pseudomonas aeruginosa.

    Science.gov (United States)

    Wang, Chan-Ju; Hagemeier, Christoph; Rahman, Nawreen; Lowe, Edward; Noble, Martin; Coughtrie, Michael; Sim, Edith; Westwood, Isaac

    2007-11-09

    The gene PA0785 from Pseudomonas aeruginosa strain PAO1, which is annotated as a probable acyl carrier protein phosphodiesterase (acpD), has been cloned and heterologously overexpressed in Escherichia coli. The purified recombinant enzyme exhibits activity corresponding to that of azoreductase but not acpD. Each recombinant protein molecule has an estimated molecular mass of 23,050 Da and one non-covalently bound FMN as co-factor. This enzyme, now identified as azoreductase 1 from Pseudomonas aeruginosa (paAzoR1), is a flavodoxin-like protein with an apparent molecular mass of 110 kDa as determined by gel-filtration chromatography, indicating that the protein is likely to be tetrameric in solution. The three-dimensional structure of paAzoR1, in complex with the substrate methyl red, was solved at a resolution of 2.18 A by X-ray crystallography. The protein exists as a dimer of dimers in the crystal lattice, with two spatially separated active sites per dimer, and the active site of paAzoR1 was shown to be a well-conserved hydrophobic pocket formed between two monomers. The paAzoR1 enzyme is able to reduce different classes of azo dyes and activate several azo pro-drugs used in the treatment of inflammatory bowel disease (IBD). During azo reduction, FMN serves as a redox centre in the electron-transferring system by mediating the electron transfer from NAD(P)H to the azo substrate. The spectral properties of paAzoR1 demonstrate the hydrophobic interaction between FMN and the active site in the protein. The structure of the ligand-bound protein also highlights the pi-stacking interactions between FMN and the azo substrate.

  18. Properties of Water Bound in Hydrogels

    Directory of Open Access Journals (Sweden)

    Vladimir M. Gun’ko

    2017-10-01

    Full Text Available In this review, the importance of water in hydrogel (HG properties and structure is analyzed. A variety of methods such as 1H NMR (nuclear magnetic resonance, DSC (differential scanning calorimetry, XRD (X-ray powder diffraction, dielectric relaxation spectroscopy, thermally stimulated depolarization current, quasi-elastic neutron scattering, rheometry, diffusion, adsorption, infrared spectroscopy are used to study water in HG. The state of HG water is rather non-uniform. According to thermodynamic features of water in HG, some of it is non-freezing and strongly bound, another fraction is freezing and weakly bound, and the third fraction is non-bound, free water freezing at 0 °C. According to structural features of water in HG, it can be divided into two fractions with strongly associated and weakly associated waters. The properties of the water in HG depend also on the amounts and types of solutes, pH, salinity, structural features of HG functionalities.

  19. X-ray structure of the NO-bound CuB in bovine cytochrome c oxidase

    Science.gov (United States)

    Ohta, Kazuhiro; Muramoto, Kazumasa; Shinzawa-Itoh, Kyoko; Yamashita, Eiki; Yoshikawa, Shinya; Tsukihara, Tomitake

    2010-01-01

    The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50 K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-reduction site, which consists of haem and a Cu atom (the haem a 3–CuB site). Electron density for the NO molecule was observed close to CuB. The refined structure indicates that NO is bound to CuB in a side-on manner. PMID:20208153

  20. Structural Model of the R State of Escherichia coli Aspartate Transcarbamoylase with Substrates Bound

    Energy Technology Data Exchange (ETDEWEB)

    Wang,J.; Eldo, J.; Kantrowitz, E.

    2007-01-01

    The allosteric enzyme aspartate transcarbamoylase (ATCase) exists in two conformational states. The enzyme, in the absence of substrates is primarily in the low-activity T state, is converted to the high-activity R state upon substrate binding, and remains in the R state until substrates are exhausted. These conformational changes have made it difficult to obtain structural data on R-state active-site complexes. Here we report the R-state structure of ATCase with the substrate Asp and the substrate analog phosphonoactamide (PAM) bound. This R-state structure represents the stage in the catalytic mechanism immediately before the formation of the covalent bond between the nitrogen of the amino group of Asp and the carbonyl carbon of carbamoyl phosphate. The binding mode of the PAM is similar to the binding mode of the phosphonate moiety of N-(phosphonoacetyl)-l-aspartate (PALA), the carboxylates of Asp interact with the same residues that interact with the carboxylates of PALA, although the position and orientations are shifted. The amino group of Asp is 2.9 {angstrom} away from the carbonyl oxygen of PAM, positioned correctly for the nucleophilic attack. Arg105 and Leu267 in the catalytic chain interact with PAM and Asp and help to position the substrates correctly for catalysis. This structure fills a key gap in the structural determination of each of the steps in the catalytic cycle. By combining these data with previously determined structures we can now visualize the allosteric transition through detailed atomic motions that underlie the molecular mechanism.

  1. 3D modeling method for computer animate based on modified weak structured light method

    Science.gov (United States)

    Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

    2010-11-01

    A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.

  2. Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome.

    Science.gov (United States)

    McGinty, Robert K; Henrici, Ryan C; Tan, Song

    2014-10-30

    The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in many eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys 119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c. However, the molecular mechanism of nucleosome substrate recognition by PRC1 or other chromatin enzymes is unclear. Here we present the crystal structure of the human Ring1B-Bmi1-UbcH5c E3-E2 complex (the PRC1 ubiquitylation module) bound to its nucleosome core particle substrate. The structure shows how a chromatin enzyme achieves substrate specificity by interacting with several nucleosome surfaces spatially distinct from the site of catalysis. Our structure further reveals an unexpected role for the ubiquitin E2 enzyme in substrate recognition, and provides insight into how the related histone H2A E3 ligase, BRCA1, interacts with and ubiquitylates the nucleosome.

  3. Topology and structure of an engineered human cohesin complex bound to Pds5B.

    Science.gov (United States)

    Hons, Michael T; Huis In 't Veld, Pim J; Kaesler, Jan; Rombaut, Pascaline; Schleiffer, Alexander; Herzog, Franz; Stark, Holger; Peters, Jan-Michael

    2016-08-23

    The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated proteins SA1/2 and Pds5A/B. Structural information is available for parts of cohesin, but analyses of entire cohesin complexes are limited by their flexibility. Here we generated a more rigid 'bonsai' cohesin by truncating the coiled coils of Smc1 and Smc3 and used single-particle electron microscopy, chemical crosslinking-mass spectrometry and in silico modelling to generate three-dimensional models of cohesin bound to Pds5B. The HEAT-repeat protein Pds5B forms a curved structure around the nucleotide-binding domains of Smc1 and Smc3 and bridges the Smc3-Scc1 and SA1-Scc1 interfaces. These results indicate that Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.

  4. Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.

    Science.gov (United States)

    Suno, Ryoji; Kimura, Kanako Terakado; Nakane, Takanori; Yamashita, Keitaro; Wang, Junmei; Fujiwara, Takaaki; Yamanaka, Yasuaki; Im, Dohyun; Horita, Shoichiro; Tsujimoto, Hirokazu; Tawaramoto, Maki S; Hirokawa, Takatsugu; Nango, Eriko; Tono, Kensuke; Kameshima, Takashi; Hatsui, Takaki; Joti, Yasumasa; Yabashi, Makina; Shimamoto, Keiko; Yamamoto, Masaki; Rosenbaum, Daniel M; Iwata, So; Shimamura, Tatsuro; Kobayashi, Takuya

    2018-01-02

    Orexin peptides in the brain regulate physiological functions such as the sleep-wake cycle, and are thus drug targets for the treatment of insomnia. Using serial femtosecond crystallography and multi-crystal data collection with a synchrotron light source, we determined structures of human orexin 2 receptor in complex with the subtype-selective antagonist EMPA (N-ethyl-2-[(6-methoxy-pyridin-3-yl)-(toluene-2-sulfonyl)-amino]-N-pyridin-3-ylmethyl-acetamide) at 2.30-Å and 1.96-Å resolution. In comparison with the non-subtype-selective antagonist suvorexant, EMPA contacted fewer residues through hydrogen bonds at the orthosteric site, explaining the faster dissociation rate. Comparisons among these OX 2 R structures in complex with selective antagonists and previously determined OX 1 R/OX 2 R structures bound to non-selective antagonists revealed that the residue at positions 2.61 and 3.33 were critical for the antagonist selectivity in OX 2 R. The importance of these residues for binding selectivity to OX 2 R was also revealed by molecular dynamics simulation. These results should facilitate the development of antagonists for orexin receptors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Crystal Structures of Free and Ligand-Bound Focal Adhesion Targeting Domain of Pyk2

    Energy Technology Data Exchange (ETDEWEB)

    Lulo, J.; Yuzawa, S; Schlessinger, J

    2009-01-01

    Focal adhesion targeting (FAT) domains target the non-receptor tyrosine kinases FAK and Pyk2 to cellular focal adhesion areas, where the signaling molecule paxillin is also located. Here, we report the crystal structures of the Pyk2 FAT domain alone or in complex with paxillin LD4 peptides. The overall structure of Pyk2-FAT is an antiparallel four-helix bundle with an up-down, up-down, right-handed topology. In the LD4-bound FAT complex, two paxillin LD4 peptides interact with two opposite sides of Pyk2-FAT, at the surfaces of the a1a4 and a2a3 helices of each FAT molecule. We also demonstrate that, while paxillin is phosphorylated by Pyk2, complex formation between Pyk2 and paxillin does not depend on Pyk2 tyrosine kinase activity. These experiments reveal the structural basis underlying the selectivity of paxillin LD4 binding to the Pyk2 FAT domain and provide insights about the molecular details which influence the different behavior of these two closely-related kinases.

  6. Structural and dynamical insights into the membrane-bound α-synuclein.

    Directory of Open Access Journals (Sweden)

    Neha Jain

    Full Text Available Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES, which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (∼ 15 Å layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could

  7. Effect of substrate on optical bound states in the continuum in 1D photonic structures

    DEFF Research Database (Denmark)

    Sadrieva, Z. F.; Sinev, I. S.; Samusev, A. K.

    2017-01-01

    Optical bound states in the continuum (BIC) are localized states with energy lying above the light line and having infinite lifetime. Any losses taking place in real systems result in transformation of the bound states into resonant states with finite lifetime. In this work, we analyze properties...... into resonant states due to leakage into the diffraction channels opening in the substrate.......Optical bound states in the continuum (BIC) are localized states with energy lying above the light line and having infinite lifetime. Any losses taking place in real systems result in transformation of the bound states into resonant states with finite lifetime. In this work, we analyze properties...

  8. Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant

    Science.gov (United States)

    Yin, Jie; Mobarec, Juan Carlos; Kolb, Peter; Rosenbaum, Daniel M.

    2015-03-01

    The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) respond to orexin neuropeptides in the central nervous system to regulate sleep and other behavioural functions in humans. Defects in orexin signalling are responsible for the human diseases of narcolepsy and cataplexy; inhibition of orexin receptors is an effective therapy for insomnia. The human OX2 receptor (OX2R) belongs to the β branch of the rhodopsin family of GPCRs, and can bind to diverse compounds including the native agonist peptides orexin-A and orexin-B and the potent therapeutic inhibitor suvorexant. Here, using lipid-mediated crystallization and protein engineering with a novel fusion chimaera, we solved the structure of the human OX2R bound to suvorexant at 2.5 Å resolution. The structure reveals how suvorexant adopts a π-stacked horseshoe-like conformation and binds to the receptor deep in the orthosteric pocket, stabilizing a network of extracellular salt bridges and blocking transmembrane helix motions necessary for activation. Computational docking suggests how other classes of synthetic antagonists may interact with the receptor at a similar position in an analogous π-stacked fashion. Elucidation of the molecular architecture of the human OX2R expands our understanding of peptidergic GPCR ligand recognition and will aid further efforts to modulate orexin signalling for therapeutic ends.

  9. Structure of the Ebola virus glycoprotein bound to a human survivor antibody

    Science.gov (United States)

    Lee, Jeffrey E.; Fusco, Marnie L.; Hessell, Ann J.; Oswald, Wendelien B.; Burton, Dennis R.; Saphire, Erica Ollmann

    2008-01-01

    Ebola virus (EBOV) entry requires the surface glycoprotein, GP, to initiate attachment and fusion of viral and host membranes. Here, we report the crystal structure of EBOV GP in its trimeric, pre-fusion conformation (GP1+GP2) bound to a neutralizing antibody, KZ52, derived from a human survivor of the 1995 Kikwit outbreak. Three GP1 viral attachment subunits assemble to form a chalice, cradled by the GP2 fusion subunits, while a novel glycan cap and projected mucin-like domain restrict access to the conserved receptor-binding site sequestered in the chalice bowl. The glycocalyx surrounding GP is likely central to immune evasion and may explain why survivors have insignificant neutralizing antibody titres. KZ52 recognizes a protein epitope at the chalice base where it clamps several regions of the pre-fusion GP2 to the N terminus of GP1. This structure now provides a template for unraveling the mechanism of EBOV GP-mediated fusion and for future immunotherapeutic development. PMID:18615077

  10. Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

    Directory of Open Access Journals (Sweden)

    Abagyan Ruben

    2002-01-01

    Full Text Available Abstract Background Nicotine is a psychoactive drug presenting a diverse array of biological activities, some positive, such as enhancement of cognitive performances, others negative, such as addiction liability. Ligands that discriminate between the different isotypes of nicotinic acetylcholine receptors (nAChRs could present improved pharmacology and toxicity profile. Results Based on the recent crystal structure of a soluble acetylcholine binding protein from snails, we have built atomic models of acetylcholine and nicotine bound to the pocket of four different human nAChR subtypes. The structures of the docked ligands correlate with available biochemical data, and reveal that the determinants for isotype selectivity are relying essentially on four residues, providing diversity of the ligand binding pocket both in terms of Van der Waals boundary, and electrostatic potential. We used our models to screen in silico a large compound database and identify a new ligand candidate that could display subtype selectivity. Conclusion The nAChR-agonist models should be useful for the design of nAChR agonists with diverse specificity profiles.

  11. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

    Energy Technology Data Exchange (ETDEWEB)

    Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. [MSKCC

    2014-08-20

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

  12. Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics

    Science.gov (United States)

    Tortora, Maxime M. C.; Doye, Jonathan P. K.

    2017-12-01

    We detail the application of bounding volume hierarchies to accelerate second-virial evaluations for arbitrary complex particles interacting through hard and soft finite-range potentials. This procedure, based on the construction of neighbour lists through the combined use of recursive atom-decomposition techniques and binary overlap search schemes, is shown to scale sub-logarithmically with particle resolution in the case of molecular systems with high aspect ratios. Its implementation within an efficient numerical and theoretical framework based on classical density functional theory enables us to investigate the cholesteric self-assembly of a wide range of experimentally relevant particle models. We illustrate the method through the determination of the cholesteric behavior of hard, structurally resolved twisted cuboids, and report quantitative evidence of the long-predicted phase handedness inversion with increasing particle thread angles near the phenomenological threshold value of 45°. Our results further highlight the complex relationship between microscopic structure and helical twisting power in such model systems, which may be attributed to subtle geometric variations of their chiral excluded-volume manifold.

  13. Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics.

    Science.gov (United States)

    Tortora, Maxime M C; Doye, Jonathan P K

    2017-12-14

    We detail the application of bounding volume hierarchies to accelerate second-virial evaluations for arbitrary complex particles interacting through hard and soft finite-range potentials. This procedure, based on the construction of neighbour lists through the combined use of recursive atom-decomposition techniques and binary overlap search schemes, is shown to scale sub-logarithmically with particle resolution in the case of molecular systems with high aspect ratios. Its implementation within an efficient numerical and theoretical framework based on classical density functional theory enables us to investigate the cholesteric self-assembly of a wide range of experimentally relevant particle models. We illustrate the method through the determination of the cholesteric behavior of hard, structurally resolved twisted cuboids, and report quantitative evidence of the long-predicted phase handedness inversion with increasing particle thread angles near the phenomenological threshold value of 45°. Our results further highlight the complex relationship between microscopic structure and helical twisting power in such model systems, which may be attributed to subtle geometric variations of their chiral excluded-volume manifold.

  14. Arthritis induces early bone high turnover, structural degradation and mechanical weakness.

    Directory of Open Access Journals (Sweden)

    Bruno Vidal

    Full Text Available We have previously found in the chronic SKG mouse model of arthritis that long standing (5 and 8 months inflammation directly leads to high collagen bone turnover, disorganization of the collagen network, disturbed bone microstructure and degradation of bone biomechanical properties. The main goal of the present work was to study the effects of the first days of the inflammatory process on the microarchitecture and mechanical properties of bone.Twenty eight Wistar adjuvant-induced arthritis (AIA rats were monitored during 22 days after disease induction for the inflammatory score, ankle perimeter and body weight. Healthy non-arthritic rats were used as controls for compar-ison. After 22 days of disease progression rats were sacrificed and bone samples were collected for histomorphometrical, energy dispersive X-ray spectroscopical analysis and 3-point bending. Blood samples were also collected for bone turnover markers.AIA rats had an increased bone turnover (as inferred from increased P1NP and CTX1, p = 0.0010 and p = 0.0002, respectively and this was paralleled by a decreased mineral content (calcium p = 0.0046 and phos-phorus p = 0.0046. Histomorphometry showed a lower trabecular thickness (p = 0.0002 and bone volume (p = 0.0003 and higher trabecular sepa-ration (p = 0.0009 in the arthritic group as compared with controls. In addition, bone mechanical tests showed evidence of fragility as depicted by diminished values of yield stress and ultimate fracture point (p = 0.0061 and p = 0.0279, re-spectively in the arthritic group.We have shown in an AIA rat model that arthritis induc-es early bone high turnover, structural degradation, mineral loss and mechanical weak-ness.

  15. Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket

    OpenAIRE

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A.; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K.

    2017-01-01

    The A2AR is a G protein-coupled receptor (GPCR) that plays important roles in cardiovascular physiology and immune function. The A2AR is also a target for the treatment of Parkinson?s disease, where A2AR antagonists have been shown to enhance signaling through the D2 dopamine receptor. Here we present the crystal structure of the A2AR bound to a novel bitopic antagonist. As a result of structural changes needed to accommodate the bound antagonist, crystals could not be grown in lipidic cubic ...

  16. Data Structure Lower Bounds on Random Access to Grammar-Compressed Strings

    DEFF Research Database (Denmark)

    Chen, Shiteng; Verbin, Elad; Yu, Wei

    2012-01-01

    ). The proof works by reduction to communication complexity, namely to the LSD problem, recently employed by Patrascu and others. We prove lower bounds also for the case of LZ-compression and Burrows-Wheeler (BWT) compression. All of our lower bounds hold even when the strings are over an alphabet of size 2...

  17. Formation of the weakly bound muonic molecule (4Heμt) 01 2 + in the three-body (tμ) 1 s +4He +4He collision

    Science.gov (United States)

    Czapliński, Wilhelm; Rybski, Michał

    2016-02-01

    Formation of the weakly bound muonic molecule (4He μt)012+ in the excited rotational-vibrational state (J , ν) = (0 , 1) due to the three-body collision (tμ)1 s +4He +4He is considered for the first time. It is assumed that the process occurs in T-4He gaseous mixture in thermal equilibrium containing thermalized muonic tritium atoms. The corresponding reaction rate is calculated in the frame of the distorted wave Born approximation (DWBA) method using the dipole approximation for the interaction of tμ +4He system with the incoming helium atom. The obtained formation rate (normalized to helium density equal to the liquid hydrogen density) increases with temperature from 7.8 ṡ106 s-1 for 1000 K to 4.8 ṡ107 s-1 for 3000 K.

  18. NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.

    Science.gov (United States)

    Güttler, Thomas; Madl, Tobias; Neumann, Piotr; Deichsel, Danilo; Corsini, Lorenzo; Monecke, Thomas; Ficner, Ralf; Sattler, Michael; Görlich, Dirk

    2010-11-01

    Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP-CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets. The different Φ spacings are compensated for by different conformations of the bound NESs: in the case of PKI, an α-helical conformation, and in the case of Rev, an extended conformation with a critical proline docking into a Φ pocket. NMR analyses of CRM1-bound and CRM1-free PKI NES suggest that CRM1 selects NES conformers that pre-exist in solution. Our data lead to a new structure-based NES consensus, and explain why NESs differ in their affinities for CRM1 and why supraphysiological NESs bind the exportin so tightly.

  19. Cell-bound lipases from Burkholderia sp. ZYB002: gene sequence analysis, expression, enzymatic characterization, and 3D structural model.

    Science.gov (United States)

    Shu, Zhengyu; Lin, Hong; Shi, Shaolei; Mu, Xiangduo; Liu, Yanru; Huang, Jianzhong

    2016-05-03

    The whole-cell lipase from Burkholderia cepacia has been used as a biocatalyst in organic synthesis. However, there is no report in the literature on the component or the gene sequence of the cell-bound lipase from this species. Qualitative analysis of the cell-bound lipase would help to illuminate the regulation mechanism of gene expression and further improve the yield of the cell-bound lipase by gene engineering. Three predictive cell-bound lipases, lipA, lipC21 and lipC24, from Burkholderia sp. ZYB002 were cloned and expressed in E. coli. Both LipA and LipC24 displayed the lipase activity. LipC24 was a novel mesophilic enzyme and displayed preference for medium-chain-length acyl groups (C10-C14). The 3D structural model of LipC24 revealed the open Y-type active site. LipA displayed 96 % amino acid sequence identity with the known extracellular lipase. lipA-inactivation and lipC24-inactivation decreased the total cell-bound lipase activity of Burkholderia sp. ZYB002 by 42 % and 14 %, respectively. The cell-bound lipase activity from Burkholderia sp. ZYB002 originated from a multi-enzyme mixture with LipA as the main component. LipC24 was a novel lipase and displayed different enzymatic characteristics and structural model with LipA. Besides LipA and LipC24, other type of the cell-bound lipases (or esterases) should exist.

  20. Purification and structural analysis of membrane-bound polyphenol oxidase from Fuji apple.

    Science.gov (United States)

    Liu, Fang; Zhao, Jin-Hong; Wen, Xin; Ni, Yuan-Ying

    2015-09-15

    Membrane-bound polyphenol oxidase (mPPO) in Fuji apple (Malus domestica Borkh. cv. Red Fuji) was purified and analyzed with a nanoelectrospray ionization mass spectrometer. The three-dimensional model and binding site of mPPO to 4-methyl catechol were also studied using molecular docking. mPPO was purified 54.41-fold using temperature-induced phase partitioning technique and ion exchange chromatography. mPPO had a molecular weight of 67.3kDa. Even though a significant level of homology was observed between mPPO and the soluble polyphenol oxidase in the copper binding sequence, there was another region, rich in histidine residues, which differed in 13 amino acids. The three-dimensional structure of mPPO consisted of six α-helices, two short β-strands, and ten random coils. The putative substrate-binding pocket contained six polar or charged amino acids, His191, His221, Trp224, Trp228, Phe227, and Val190. Trp224 and Trp228 formed hydrogen bonds with 4-methyl-catechol. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Chirped-Pulse Fourier-Transform Microwave Spectroscopy of the Prototypical C-H\\cdotsπ Interaction: the BENZENE\\cdotsACETYLENE Weakly Bound Dimer

    Science.gov (United States)

    Ulrich, Nathan; Seifert, Nathan A.; Dorris, Rachel E.; Peebles, Rebecca A.; Peebles, Sean A.; Pate, Brooks

    2014-06-01

    The rotational spectrum of the CH\\cdotsπ bonded complex between benzene and acetylene has been measured in the 6-20 GHz range using chirped-pulse Fourier-transform microwave spectroscopy. The spectra for the normal isotopologue, three unique 13C substituted species, and the d_1-benzene\\cdotsHCCH species have allowed determination of the dimer structure. The spectrum is that of a symmetric top, with effective C6v symmetry, and a CH\\cdotsπ distance of 2.4921(1) Å. The dipole moment has been measured using the Stark effect, and is 0.438(11) D. In addition to the ground state spectrum, three additional sets of transitions corresponding to similar rotational constants have been observed, likely due to excitation of the three low energy intermolecular vibrational modes of the dimer. Analysis of these excited state transitions is in progress. Comparison of the binding energy and structure of the benzene\\cdotsHCCH dimer with other H\\cdotsπ complexes will be presented.

  2. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.

    Science.gov (United States)

    Gagnon, Matthieu G; Seetharaman, Sai V; Bulkley, David; Steitz, Thomas A

    2012-03-16

    In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.

  3. Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates

    Science.gov (United States)

    Gwon, Gwang Hyeon; Jo, Aera; Baek, Kyuwon; Jin, Kyeong Sik; Fu, Yaoyao; Lee, Jong-Bong; Kim, YoungChang; Cho, Yunje

    2014-01-01

    The Mus81-Eme1 complex is a structure-selective endonuclease with a critical role in the resolution of recombination intermediates during DNA repair after interstrand cross-links, replication fork collapse, or double-strand breaks. To explain the molecular basis of 3′ flap substrate recognition and cleavage mechanism by Mus81-Eme1, we determined crystal structures of human Mus81-Eme1 bound to various flap DNA substrates. Mus81-Eme1 undergoes gross substrate-induced conformational changes that reveal two key features: (i) a hydrophobic wedge of Mus81 that separates pre- and post-nick duplex DNA and (ii) a “5′ end binding pocket” that hosts the 5′ nicked end of post-nick DNA. These features are crucial for comprehensive protein-DNA interaction, sharp bending of the 3′ flap DNA substrate, and incision strand placement at the active site. While Mus81-Eme1 unexpectedly shares several common features with members of the 5′ flap nuclease family, the combined structural, biochemical, and biophysical analyses explain why Mus81-Eme1 preferentially cleaves 3′ flap DNA substrates with 5′ nicked ends. PMID:24733841

  4. Structural Basis for the Rescue of Stalled Ribosomes: Structure of YaeJ Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gagnon, Matthieu G.; Seetharaman, Sai V.; Bulkley, David; Steitz, Thomas A. (Yale)

    2012-06-19

    In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA{sub i}{sup fMet} and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.

  5. Substrate-bound structures of benzylsuccinate synthase reveal how toluene is activated in anaerobic hydrocarbon degradation.

    Science.gov (United States)

    Funk, Michael A; Marsh, E Neil G; Drennan, Catherine L

    2015-09-11

    Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C-C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these "X-succinate synthases" and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation*

    Science.gov (United States)

    Funk, Michael A.; Marsh, E. Neil G.; Drennan, Catherine L.

    2015-01-01

    Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C—C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C—C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these “X-succinate synthases” and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes. PMID:26224635

  7. The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2

    Directory of Open Access Journals (Sweden)

    Winger Jonathan A

    2009-02-01

    Full Text Available Abstract Background Imatinib represents the first in a class of drugs targeted against chronic myelogenous leukemia to enter the clinic, showing excellent efficacy and specificity for Abl, Kit, and PDGFR kinases. Recent screens carried out to find off-target proteins that bind to imatinib identified the oxidoreductase NQO2, a flavoprotein that is phosphorylated in a chronic myelogenous leukemia cell line. Results We examined the inhibition of NQO2 activity by the Abl kinase inhibitors imatinib, nilotinib, and dasatinib, and obtained IC50 values of 80 nM, 380 nM, and >100 μM, respectively. Using electronic absorption spectroscopy, we show that imatinib binding results in a perturbation of the protein environment around the flavin prosthetic group in NQO2. We have determined the crystal structure of the complex of imatinib with human NQO2 at 1.75 Å resolution, which reveals that imatinib binds in the enzyme active site, adjacent to the flavin isoalloxazine ring. We find that phosphorylation of NQO2 has little effect on enzyme activity and is therefore likely to regulate other aspects of NQO2 function. Conclusion The structure of the imatinib-NQO2 complex demonstrates that imatinib inhibits NQO2 activity by competing with substrate for the active site. The overall conformation of imatinib when bound to NQO2 resembles the folded conformation observed in some kinase complexes. Interactions made by imatinib with residues at the rim of the active site provide an explanation for the binding selectivity of NQO2 for imatinib, nilotinib, and dasatinib. These interactions also provide a rationale for the lack of inhibition of the related oxidoreductase NQO1 by these compounds. Taken together, these studies provide insight into the mechanism of NQO2 inhibition by imatinib, with potential implications for drug design and treatment of chronic myelogenous leukemia in patients.

  8. Analysis, structure and geochemical significance of organically-bound sulphur in the geosphere : State of the art and future research

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Leeuw, J.W. de

    1990-01-01

    This paper reviews the developments of the 1980s in the characterisation of organically-bound sulphur in the geosphere and summarises the geochemical significance of the results obtained by these studies. The identification of more than 1500 novel OSC (organic sulphur compounds) with structures

  9. Three-dimensional structured illumination microscopy using Lukosz bound apodization reduces pixel negativity at no resolution cost

    NARCIS (Netherlands)

    Righolt, C.H.; Mai, S.; Van Vliet, L.J.; Stallinga, S.

    2014-01-01

    The quality of the reconstructed image in structured illumination microscopy (SIM) depends on various aspects of the image filtering process. To optimize the trade-off between resolution and ringing artifacts, which lead to negative intensities, we extend Lukosz-bound filtering to 3D SIM and derive

  10. Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins.

    Science.gov (United States)

    Mihailescu, Mihail; Meirovitch, Hagai

    2010-08-25

    A mobile loop changes its conformation from "open" (free enzyme) to "closed" upon ligand binding. The difference in the Helmholtz free energy, ΔF(loop) between these states sheds light on the mechanism of binding. With our "hypothetical scanning molecular dynamics" (HSMD-TI) method ΔF(loop) = F(free) - F(bound) where F(free) and F(bound) are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI) procedure. In previous work the free and bound loop structures were both attached to the same "template" which was "cut" from the crystal structure of the free protein. Our results for loop 287-290 of AcetylCholineEsterase agree with the experiment, ΔF(loop)~ -4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., N(water) = 140 - 180 waters in a sphere of a 18 Å radius. Here we calculate ΔF(loop) for the more realistic case, where two templates are "cut" from the crystal structures, 2dfp.pdb (bound) and 2ace.pdb (free), where N(water) = 40 - 160; this requires adding a computationally more demanding (second) TI procedure. While the results for N(water) ≤ 140 are computationally sound, ΔF(loop) is always positive (18 ± 2 kcal/mol for N(water) = 140). These (disagreeing) results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å(2) for 2ace). While this conformational uncertainty is an inherent difficulty, the (unstable) results for N(water) = 160 suggest that it might be alleviated by applying different (initial) structural optimizations to each template.

  11. Crystal structure of the adenosine A2Areceptor bound to an antagonist reveals a potential allosteric pocket.

    Science.gov (United States)

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K

    2017-02-21

    The adenosine A 2A receptor (A 2A R) has long been implicated in cardiovascular disorders. As more selective A 2A R ligands are being identified, its roles in other disorders, such as Parkinson's disease, are starting to emerge, and A 2A R antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A 2A receptor bound to compound 1 (Cmpd-1), a novel A 2A R/ N -methyl d-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A 2A receptor with a cytochrome b562-RIL (BRIL) fusion (A 2A R-BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A 2A R-BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1-bound A 2A R-BRIL prevented formation of the lattice observed with the ZM241385-bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A 2A R structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr9 1.35 and Tyr271 7.36 , which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A 2A R structures, highlighting flexibility in the binding pocket that may facilitate the development of A 2A R-selective compounds for the treatment of Parkinson's disease.

  12. Angular structure of jet quenching within a hybrid strong/weak coupling model

    Energy Technology Data Exchange (ETDEWEB)

    Casalderrey-Solana, Jorge [Rudolf Peierls Centre for Theoretical Physics, University of Oxford,1 Keble Road, Oxford OX1 3NP (United Kingdom); Departament de Física Quàntica i Astrofísica & Institut de Ciències del Cosmos (ICC),Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Gulhan, Doga Can [CERN, EP Department,CH-1211 Geneva 23 (Switzerland); Milhano, José Guilherme [CENTRA, Instituto Superior Técnico, Universidade de Lisboa,Av. Rovisco Pais, P-1049-001 Lisboa (Portugal); Laboratório de Instrumentação e Física Experimental de Partículas (LIP),Av. Elias Garcia 14-1, P-1000-149 Lisboa (Portugal); Theoretical Physics Department, CERN,Geneva (Switzerland); Pablos, Daniel [Departament de Física Quàntica i Astrofísica & Institut de Ciències del Cosmos (ICC),Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Rajagopal, Krishna [Center for Theoretical Physics, Massachusetts Institute of Technology,Cambridge, MA 02139 (United States)

    2017-03-27

    Within the context of a hybrid strong/weak coupling model of jet quenching, we study the modification of the angular distribution of the energy within jets in heavy ion collisions, as partons within jet showers lose energy and get kicked as they traverse the strongly coupled plasma produced in the collision. To describe the dynamics transverse to the jet axis, we add the effects of transverse momentum broadening into our hybrid construction, introducing a parameter K≡q̂/T{sup 3} that governs its magnitude. We show that, because of the quenching of the energy of partons within a jet, even when K≠0 the jets that survive with some specified energy in the final state are narrower than jets with that energy in proton-proton collisions. For this reason, many standard observables are rather insensitive to K. We propose a new differential jet shape ratio observable in which the effects of transverse momentum broadening are apparent. We also analyze the response of the medium to the passage of the jet through it, noting that the momentum lost by the jet appears as the momentum of a wake in the medium. After freezeout this wake becomes soft particles with a broad angular distribution but with net momentum in the jet direction, meaning that the wake contributes to what is reconstructed as a jet. This effect must therefore be included in any description of the angular structure of the soft component of a jet. We show that the particles coming from the response of the medium to the momentum and energy deposited in it leads to a correlation between the momentum of soft particles well separated from the jet in angle with the direction of the jet momentum, and find qualitative but not quantitative agreement with experimental data on observables designed to extract such a correlation. More generally, by confronting the results that we obtain upon introducing transverse momentum broadening and the response of the medium to the jet with available jet data, we highlight the

  13. Quadriceps Weakness, Patella Alta and Structural Features of Patellofemoral Osteoarthritis: The Multicenter Osteoarthritis Study

    Science.gov (United States)

    Stefanik, Joshua J.; Guermazi, Ali; Zhu, Yanyan; Zumwalt, Ann C.; Gross, K. Douglas; Clancy, Margaret; Lynch, John A.; Segal, Neil A.; Lewis, Cora E.; Roemer, Frank W.; Powers, Christopher M.; Felson, David T.

    2011-01-01

    Objective To determine the relationship between quadriceps weakness and cartilage damage and bone marrow lesions (BMLs) in the patellofemoral joint (PFJ), and if this relationship is modified by patella alta. Methods The Multicenter Osteoarthritis (MOST) Study is a cohort study of persons aged 50–79 years with or at risk for knee OA. Concentric knee extensor strength was measured using an isokinetic dynamometer. Patella alta was measured using the Insall-Salvati ratio (ISR) on the lateral radiograph, and cartilage damage and bone marrow lesions (BMLs) were graded on MRI in the PFJ. We determined the association between quadriceps weakness with cartilage damage and BMLs in the PFJ among those knees with (ISR≥1.2) and without patella alta (ISRpatella alta in the lateral PFJ. Conclusion Quadriceps weakness was associated with PFJ cartilage damage and BMLs. While both patella alta and quadriceps weakness are associated with PFJ damage, the combination of the two was not associated with more damage than either of these factors alone. PMID:21702087

  14. Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain.

    Science.gov (United States)

    Ogawa, Haruo; Shinoda, Takehiro; Cornelius, Flemming; Toyoshima, Chikashi

    2009-08-18

    The sodium-potassium pump (Na(+),K(+)-ATPase) is responsible for establishing Na(+) and K(+) concentration gradients across the plasma membrane and therefore plays an essential role in, for instance, generating action potentials. Cardiac glycosides, prescribed for congestive heart failure for more than 2 centuries, are efficient inhibitors of this ATPase. Here we describe a crystal structure of Na(+),K(+)-ATPase with bound ouabain, a representative cardiac glycoside, at 2.8 A resolution in a state analogous to E2.2K(+).Pi. Ouabain is deeply inserted into the transmembrane domain with the lactone ring very close to the bound K(+), in marked contrast to previous models. Due to antagonism between ouabain and K(+), the structure represents a low-affinity ouabain-bound state. Yet, most of the mutagenesis data obtained with the high-affinity state are readily explained by the present crystal structure, indicating that the binding site for ouabain is essentially the same. According to a homology model for the high affinity state, it is a closure of the binding cavity that confers a high affinity.

  15. Bound-state field-theory approach to proton-structure effects in muonic hydrogen

    Science.gov (United States)

    Mohr, Peter J.; Griffith, J.; Sapirstein, J.

    2013-05-01

    A bound-state field-theory approach to muonic hydrogen is set up using a variant of the Furry representation in which the lowest-order Hamiltonian describes a muon in the presence of a point Coulomb field, but the origin of the binding field is taken to be three charged quarks in the proton, which are modeled as Dirac particles that move freely within a spherical well. Bound-state field-theory techniques are used to evaluate one- and two-photon effects. Particular attention is paid to two-photon-exchange diagrams, which include the effect of proton polarizability. In addition, the modification of the electromagnetic self energy of the proton by the electric field of the muon is examined. Finally, the model is used to carry out a calculation of the static electric polarizability of the proton.

  16. Secondary Interactions Involving Zinc-Bound Ligands: Roles in Structural Stabilization and Macromolecular Interactions

    OpenAIRE

    Namuswe, Frances; Berg, Jeremy M.

    2011-01-01

    A large number of proteins contain bound zinc ions. These zinc ions are frequently coordinated by a combination of histidine and cysteine residues. In addition to atoms that coordinate directly to the zinc ions, these side chains have groups that can donate or accept hydrogen bonds from other groups. These secondary interactions can help stabilize the zinc-binding sites, can contribute to protein folding and stability, and, on occasion, can participate in interactions with other macromolecule...

  17. Electromagnetic structure and weak decay of meson K in a light-front QCD-inspired

    CERN Document Server

    Pereira, Fabiano P; Frederico, T; Tomio, Lauro

    2007-01-01

    The kaon electromagnetic (e.m.) form factor is reviewed considering a light-front constituent quark model. In this approach, it is discussed the relevance of the quark-antiquark pair terms for the full covariance of the e.m. current. It is also verified, by considering a QCD dynamical model, that a good agreement with experimental data can be obtained for the kaon weak decay constant once a probability of about 80% of the valence component is taken into account.

  18. Power Flow Calculation for Weakly Meshed Distribution Networks with Multiple DGs Based on Generalized Chain-table Storage Structure

    DEFF Research Database (Denmark)

    Chen, Shuheng; Hu, Weihao; Chen, Zhe

    2014-01-01

    Based on generalized chain-table storage structure (GCTSS), a novel power flow method is proposed, which can be used to solve the power flow of weakly meshed distribution networks with multiple distributed generators (DGs). GCTSS is designed based on chain-table technology and its target is to de......Based on generalized chain-table storage structure (GCTSS), a novel power flow method is proposed, which can be used to solve the power flow of weakly meshed distribution networks with multiple distributed generators (DGs). GCTSS is designed based on chain-table technology and its target...... is to describe the topology of radial distribution networks with a clear logic and a small memory size. The strategies of compensating the equivalent currents of break-point branches and the reactive power outputs of PV-type DGs are presented on the basis of superposition theorem. Their formulations...

  19. Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State

    Directory of Open Access Journals (Sweden)

    Yoshiki Tanaka

    2015-11-01

    Full Text Available The bacterial SecYEG translocon functions as a conserved protein-conducting channel. Conformational transitions of SecYEG allow protein translocation across the membrane without perturbation of membrane permeability. Here, we report the crystal structures of intact SecYEG at 2.7-Å resolution and of peptide-bound SecYEG at 3.6-Å resolution. The higher-resolution structure revealed that the cytoplasmic loop of SecG covers the hourglass-shaped channel, which was confirmed to also occur in the membrane by disulfide bond formation analysis and molecular dynamics simulation. The cytoplasmic loop may be involved in protein translocation. In addition, the previously unknown peptide-bound crystal structure of SecYEG implies that interactions between the cytoplasmic side of SecY and signal peptides are related to lateral gate opening at the first step of protein translocation. These SecYEG structures therefore provide a number of structural insights into the Sec machinery for further study.

  20. Structural evidence for a copper-bound carbonate intermediate in the peroxidase and dismutase activities of superoxide dismutase.

    Science.gov (United States)

    Strange, Richard W; Hough, Michael A; Antonyuk, Svetlana V; Hasnain, S Samar

    2012-01-01

    Copper-zinc superoxide dismutase (SOD) is of fundamental importance to our understanding of oxidative damage. Its primary function is catalysing the dismutation of superoxide to O(2) and H(2)O(2). SOD also reacts with H(2)O(2), leading to the formation of a strong copper-bound oxidant species that can either inactivate the enzyme or oxidise other substrates. In the presence of bicarbonate (or CO(2)) and H(2)O(2), this peroxidase activity is enhanced and produces the carbonate radical. This freely diffusible reactive oxygen species is proposed as the agent for oxidation of large substrates that are too bulky to enter the active site. Here, we provide direct structural evidence, from a 2.15 Å resolution crystal structure, of (bi)carbonate captured at the active site of reduced SOD, consistent with the view that a bound carbonate intermediate could be formed, producing a diffusible carbonate radical upon reoxidation of copper. The bound carbonate blocks direct access of substrates to Cu(I), suggesting that an adjunct to the accepted mechanism of SOD catalysed dismutation of superoxide operates, with Cu(I) oxidation by superoxide being driven via a proton-coupled electron transfer mechanism involving the bound carbonate rather than the solvent. Carbonate is captured in a different site when SOD is oxidised, being located in the active site channel adjacent to the catalytically important Arg143. This is the probable route of diffusion from the active site following reoxidation of the copper. In this position, the carbonate is poised for re-entry into the active site and binding to the reduced copper.

  1. Structural evidence for a copper-bound carbonate intermediate in the peroxidase and dismutase activities of superoxide dismutase.

    Directory of Open Access Journals (Sweden)

    Richard W Strange

    Full Text Available Copper-zinc superoxide dismutase (SOD is of fundamental importance to our understanding of oxidative damage. Its primary function is catalysing the dismutation of superoxide to O(2 and H(2O(2. SOD also reacts with H(2O(2, leading to the formation of a strong copper-bound oxidant species that can either inactivate the enzyme or oxidise other substrates. In the presence of bicarbonate (or CO(2 and H(2O(2, this peroxidase activity is enhanced and produces the carbonate radical. This freely diffusible reactive oxygen species is proposed as the agent for oxidation of large substrates that are too bulky to enter the active site. Here, we provide direct structural evidence, from a 2.15 Å resolution crystal structure, of (bicarbonate captured at the active site of reduced SOD, consistent with the view that a bound carbonate intermediate could be formed, producing a diffusible carbonate radical upon reoxidation of copper. The bound carbonate blocks direct access of substrates to Cu(I, suggesting that an adjunct to the accepted mechanism of SOD catalysed dismutation of superoxide operates, with Cu(I oxidation by superoxide being driven via a proton-coupled electron transfer mechanism involving the bound carbonate rather than the solvent. Carbonate is captured in a different site when SOD is oxidised, being located in the active site channel adjacent to the catalytically important Arg143. This is the probable route of diffusion from the active site following reoxidation of the copper. In this position, the carbonate is poised for re-entry into the active site and binding to the reduced copper.

  2. Helical structure of longitudinal vortices embedded in turbulent wall-bounded flow

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Hansen, Martin Otto Laver; Okulov, Valery

    2009-01-01

    Embedded vortices in turbulent wall-bounded flow over a flat plate, generated by a passive rectangular vane-type vortex generator with variable angle \\beta to the incoming flow in a low-Reynolds number flow (Re = 2600 based on the inlet grid mesh size L = 0:039 m and free stream velocity U......_{\\infty} = 1.0 ms^{-1}) have been studied with respect to helical symmetry. The studies were carried out in a low-speed closed-circuit wind tunnel utilizing Stereoscopic Particle Image Velocimetry (SPIV). The vortices have been shown to possess helical symmetry, allowing the flow to be described in a simple...

  3. Strong and weak, unsteady reconfiguration and its impact on turbulence structure within plant canopies

    Science.gov (United States)

    Pan, Ying; Follett, Elizabeth; Chamecki, Marcelo; Nepf, Heidi

    2014-10-01

    Flexible terrestrial and aquatic plants bend in response to fluid motion and this reconfiguration mechanism reduces drag forces, which protects against uprooting or breaking under high winds and currents. The impact of reconfiguration on the flow can be described quantitatively by introducing a drag coefficient that decreases as a power-law function of velocity with a negative exponent known as the Vogel number. In this paper, two case studies are conducted to examine the connection between reconfiguration and turbulence dynamics within a canopy. First, a flume experiment was conducted with a model seagrass meadow. As the flow rate increased, both the mean and unsteady one-dimensional linear elastic reconfiguration increased. In the transition between the asymptotic regimes of negligible and strong reconfiguration, there is a regime of weak reconfiguration, in which the Vogel number achieved its peak negative value. Second, large-eddy simulation was conducted for a maize canopy, with different modes of reconfiguration characterized by increasingly negative values of the Vogel number. Even though the mean vertical momentum flux was constrained by field measurements, changing the mode of reconfiguration altered the distribution, strength, and fraction of momentum carried by strong and weak events. Despite the differences between these two studies, similar effects of the Vogel number on turbulence dynamics were demonstrated. In particular, a more negative Vogel number leads to a more positive peak of the skewness of streamwise velocity within the canopy, which indicates a preferential penetration of strong events into a vegetation canopy. We consider different reconfiguration geometry (one- and two-dimensional) and regime (negligible, weak, and strong) that can apply to a wide range of terrestrial and aquatic canopies.

  4. Two particle nonleptonic decays of D and F mesons and the structure of weak interactions

    CERN Document Server

    Voloshin, M B; Okun, Lev Borisovich

    1975-01-01

    The two particle nonleptonic decays of charmed D/sup +or-/, D/sup 0/, D/sup approximately 0/ and F/sup +or-/ mesons are examined within the framework of a unitary symmetry. The ratios between the amplitudes of various different decays, resulting from the unitary symmetry and the assumption that the hamiltonian of weak interactions takes the form of the product of the current multiplied by the current, are found. The consequences of the T-, U- and V-spin selection rules are considered. (9 refs).

  5. Angular Structure of Jet Quenching Within a Hybrid Strong/Weak Coupling Model

    CERN Document Server

    Casalderrey-Solana, Jorge; Milhano, Guilherme; Pablos, Daniel; Rajagopal, Krishna

    2017-01-01

    Within the context of a hybrid strong/weak coupling model of jet quenching, we study the modification of the angular distribution of the energy within jets in heavy ion collisions, as partons within jet showers lose energy and get kicked as they traverse the strongly coupled plasma produced in the collision. To describe the dynamics transverse to the jet axis, we add the effects of transverse momentum broadening into our hybrid construction, introducing a parameter $K\\equiv \\hat q/T^3$ that governs its magnitude. We show that, because of the quenching of the energy of partons within a jet, even when $K\

  6. Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins

    Directory of Open Access Journals (Sweden)

    Hagai Meirovitch

    2010-08-01

    Full Text Available A mobile loop changes its conformation from “open” (free enzyme to “closed” upon ligand binding. The difference in the Helmholtz free energy, ΔFloop between these states sheds light on the mechanism of binding. With our “hypothetical scanning molecular dynamics” (HSMD-TI method ΔFloop = Ffree − Fbound where Ffree and Fbound are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI procedure. In previous work the free and bound loop structures were both attached to the same “template” which was “cut” from the crystal structure of the free protein. Our results for loop 287−290 of AcetylCholineEsterase agree with the experiment, ΔFloop~ −4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., Nwater = 140 − 180 waters in a sphere of a 18 Å radius. Here we calculate ΔFloop for the more realistic case, where two templates are “cut” from the crystal structures, 2dfp.pdb (bound and 2ace.pdb (free, where Nwater = 40 − 160; this requires adding a computationally more demanding (second TI procedure. While the results for Nwater ≤ 140 are computationally sound, ΔFloop is always positive (18 ± 2 kcal/mol for Nwater = 140. These (disagreeing results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å2 for 2ace. While this conformational uncertainty is an inherent difficulty, the (unstable results for Nwater = 160 suggest that it might be alleviated by applying different (initial structural optimizations to each template.

  7. Bounded Confidence under Preferential Flip: A Coupled Dynamics of Structural Balance and Opinions.

    Science.gov (United States)

    Parravano, Antonio; Andina-Díaz, Ascensión; Meléndez-Jiménez, Miguel A

    2016-01-01

    In this work we study the coupled dynamics of social balance and opinion formation. We propose a model where agents form opinions under bounded confidence, but only considering the opinions of their friends. The signs of social ties -friendships and enmities- evolve seeking for social balance, taking into account how similar agents' opinions are. We consider both the case where opinions have one and two dimensions. We find that our dynamics produces the segregation of agents into two cliques, with the opinions of agents in one clique differing from those in the other. Depending on the level of bounded confidence, the dynamics can produce either consensus of opinions within each clique or the coexistence of several opinion clusters in a clique. For the uni-dimensional case, the opinions in one clique are all below the opinions in the other clique, hence defining a "left clique" and a "right clique". In the two-dimensional case, our numerical results suggest that the two cliques are separated by a hyperplane in the opinion space. We also show that the phenomenon of unidimensional opinions identified by DeMarzo, Vayanos and Zwiebel (Q J Econ 2003) extends partially to our dynamics. Finally, in the context of politics, we comment about the possible relation of our results to the fragmentation of an ideology and the emergence of new political parties.

  8. Bounded Confidence under Preferential Flip: A Coupled Dynamics of Structural Balance and Opinions.

    Directory of Open Access Journals (Sweden)

    Antonio Parravano

    Full Text Available In this work we study the coupled dynamics of social balance and opinion formation. We propose a model where agents form opinions under bounded confidence, but only considering the opinions of their friends. The signs of social ties -friendships and enmities- evolve seeking for social balance, taking into account how similar agents' opinions are. We consider both the case where opinions have one and two dimensions. We find that our dynamics produces the segregation of agents into two cliques, with the opinions of agents in one clique differing from those in the other. Depending on the level of bounded confidence, the dynamics can produce either consensus of opinions within each clique or the coexistence of several opinion clusters in a clique. For the uni-dimensional case, the opinions in one clique are all below the opinions in the other clique, hence defining a "left clique" and a "right clique". In the two-dimensional case, our numerical results suggest that the two cliques are separated by a hyperplane in the opinion space. We also show that the phenomenon of unidimensional opinions identified by DeMarzo, Vayanos and Zwiebel (Q J Econ 2003 extends partially to our dynamics. Finally, in the context of politics, we comment about the possible relation of our results to the fragmentation of an ideology and the emergence of new political parties.

  9. Optimization strategy for and structural properties of traffic efficiency under bounded information accessibility

    Science.gov (United States)

    Sanghyun, Ahn; Seungwoong, Ha; Kim, Soo Yong

    2016-06-01

    A vital challenge for many socioeconomic systems is determining the optimum use of limited information. Traffic systems, wherein the range of resources is limited, are a particularly good example of this challenge. Based on bounded information accessibility in terms of, for example, high costs or technical limitations, we develop a new optimization strategy to improve the efficiency of a traffic system with signals and intersections. Numerous studies, including the study by Chowdery and Schadschneider (whose method we denote by ChSch), have attempted to achieve the maximum vehicle speed or the minimum wait time for a given traffic condition. In this paper, we introduce a modified version of ChSch with an independently functioning, decentralized control system. With the new model, we determine the optimization strategy under bounded information accessibility, which proves the existence of an optimal point for phase transitions in the system. The paper also provides insight that can be applied by traffic engineers to create more efficient traffic systems by analyzing the area and symmetry of local sites. We support our results with a statistical analysis using empirical traffic data from Seoul, Korea.

  10. Protease inhibitors, part 13: Specific, weakly basic thrombin inhibitors incorporating sulfonyl dicyandiamide moieties in their structure.

    Science.gov (United States)

    Clare, B W; Scozzafava, A; Supuran, C T

    2001-01-01

    A series of compounds has been prepared by reaction of dicyandiamide with alkyl/arylsulfonyl halides as well as arylsulfonylisocyanates to locate a lead for obtaining weakly basic thrombin inhibitors with sulfonyldicyandiamide moieties as the S1 anchoring group. The detected lead was sulfanilyl-dicyandiamide (K1 of 3 microM against thrombin, and 15 microM against trypsin), which has been further derivatized at the 4-amino group by incorporating arylsulfonylureido as well as amino acyl/dipeptidyl groups protected at the amino terminal moiety with benzyloxycarbonyl or tosylureido moieties. The best compound obtained (ts-D-Phe-Pro-sulfanilyl-dicyandiamide) showed inhibition constants of 9 nM against thrombin and 1400 nM against trypsin. pKa measurements showed that the new derivatives reported here do indeed possess a reduced basicity, with the pKa of the modified guanidine moieties in the range 7.9-8.3 pKa units. Molecular mechanics calculations showed that the preferred tautomeric form of these compounds is of the type ArSO2N=C(NH2) NH-CN, probably allowing for the formation of favorable interaction between this new anchoring group and the active site amino acid residue Asp 189, critical for substrate/inhibitor binding to this type of serine protease. Thus, the main finding of the present paper is that the sulfonyldicyandiamide group may constitute an interesting alternative for obtaining weakly basic, potent thrombin inhibitors, which bind with less affinity to trypsin.

  11. Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)

    2014-09-19

    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

  12. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Bradley R.; Drake, Eric J.; Shi, Ce; Aldrich, Courtney C.; Gulick, Andrew M. (UMM); (HWMRI)

    2016-09-05

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa. These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.

  13. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture.

    Science.gov (United States)

    Miller, Bradley R; Drake, Eric J; Shi, Ce; Aldrich, Courtney C; Gulick, Andrew M

    2016-10-21

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Mechanism of the Quorum-Quenching Lactonase (AiiA) from Bacillus thuringiensis. 1. Product-Bound Structures

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Dali; Momb, Jessica; Thomas, Pei W.; Moulin, Aaron; Petsko, Gregory A.; Fast, Walter; Ringe, Dagmar (Brandeis); (Texas)

    2008-08-06

    Enzymes capable of hydrolyzing N-acyl-l-homoserine lactones (AHLs) used in some bacterial quorum-sensing pathways are of considerable interest for their ability to block undesirable phenotypes. Most known AHL hydrolases that catalyze ring opening (AHL lactonases) are members of the metallo-{beta}-lactamase enzyme superfamily and rely on a dinuclear zinc site for catalysis and stability. Here we report the three-dimensional structures of three product complexes formed with the AHL lactonase from Bacillus thuringiensis. Structures of the lactonase bound with two different concentrations of the ring-opened product of N-hexanoyl-l-homoserine lactone are determined at 0.95 and 1.4 {angstrom} resolution and exhibit different product configurations. A structure of the ring-opened product of the non-natural N-hexanoyl-l-homocysteine thiolactone at 1.3 {angstrom} resolution is also determined. On the basis of these product-bound structures, a substrate-binding model is presented that differs from previous proposals. Additionally, the proximity of the product to active-site residues and observed changes in protein conformation and metal coordination provide insight into the catalytic mechanism of this quorum-quenching metalloenzyme.

  15. Weakly nonlinear dispersion and stop-band effects for periodic structures

    DEFF Research Database (Denmark)

    Sorokin, Vladislav; Thomsen, Jon Juel

    of engineering periodic structures include some building frames, bridge trusses, cranes, railway tracks, and compound pipes. Thus dynamic analysis of spatially periodic structures is relevant for many applications, and attracts much attention. An essential feature of periodic structures is the presence...

  16. Asymptotic structure of N=2 supergravity in 3D: extended super-BMS3 and nonlinear energy bounds

    Science.gov (United States)

    Fuentealba, Oscar; Matulich, Javier; Troncoso, Ricardo

    2017-09-01

    The asymptotically flat structure of N=(2,0) supergravity in three spacetime dimensions is explored. The asymptotic symmetries are found to be spanned by an extension of the super-BMS3 algebra, endowed with two independent affine û(1) currents of electric and magnetic type. These currents are associated to U(1) fields being even and odd under parity, respectively. Remarkably, although the U(1) fields do not generate a backreaction on the metric, they provide nontrivial Sugawara-like contributions to the BMS3 generators, and hence to the energy and the angular momentum. Consequently, the entropy of flat cosmological spacetimes endowed with U(1) fields acquires a nontrivial dependence on the zero modes of the û(1) charges. If the spin structure is odd, the ground state corresponds to Minkowski spacetime, and although the anticommutator of the canonical supercharges is linear in the energy and in the electric-like û(1) charge, the energy becomes bounded from below by the energy of the ground state shifted by the square of the electric-like û(1) charge. If the spin structure is even, the same bound for the energy generically holds, unless the absolute value of the electric-like charge is less than minus the mass of Minkowski spacetime in vacuum, so that the energy has to be nonnegative. The explicit form of the global and asymptotic Killing spinors is found for a wide class of configurations that fulfills our boundary conditions, and they exist precisely when the corresponding bounds are saturated. It is also shown that the spectra with periodic or antiperiodic boundary conditions for the fermionic fields are related by spectral flow, in a similar way as it occurs for the N=2 super-Virasoro algebra. Indeed, our supersymmetric extension of BMS3 can be recovered from the Inönü-Wigner contraction of the superconformal algebra with N=(2,2) , once the fermionic generators of the right copy are truncated.

  17. Mapping the orbital structure of impurity bound states in a superconductor.

    Science.gov (United States)

    Choi, Deung-Jang; Rubio-Verdú, Carmen; de Bruijckere, Joeri; Ugeda, Miguel M; Lorente, Nicolás; Pascual, Jose Ignacio

    2017-05-08

    A magnetic atom inside a superconductor locally distorts superconductivity. It scatters Cooper pairs as a potential with broken time-reversal symmetry, leading to localized bound states with subgap excitation energies, named Shiba states. Most conventional approaches regarding Shiba states treat magnetic impurities as point scatterers with isotropic exchange interaction. Here, we show that the number and the shape of Shiba states are correlated to the spin-polarized atomic orbitals of the impurity, hybridized with the superconductor. Using scanning tunnelling spectroscopy, we spatially map the five Shiba excitations found on subsurface chromium atoms in Pb(111), resolving their particle and hole components. While particle components resemble d orbitals of embedded Cr atoms, hole components differ strongly from them. Density functional theory simulations correlate the orbital shapes to the magnetic ground state of the atom, and identify scattering channels and interactions, all valuable tools for designing atomic-scale superconducting devices.

  18. Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor

    DEFF Research Database (Denmark)

    Svensson, L Anders; Bondensgaard, Kent; Nørskov-Lauritsen, Leif

    2008-01-01

    The crystal structure of the complex between an N-terminally truncated G129R human prolactin (PRL) variant and the extracellular domain of the human prolactin receptor (PRLR) was determined at 2.5A resolution by x-ray crystallography. This structure represents the first experimental structure...

  19. Augmented weak forms and element-by-element preconditioners: Efficient iterative strategies for structural finite elements. A preliminary study

    Science.gov (United States)

    Muller, A.; Hughes, T. J. R.

    1984-01-01

    A weak formulation in structural analysis that provides well conditioned matrices suitable for iterative solutions is presented. A mixed formulation ensures the proper representation of the problem and the constitutive relations are added in a penalized form. The problem is solved by a double conjugate gradient algorithm combined with an element by element approximate factorization procedure. The double conjugate gradient strategy resembles Uzawa's variable-length type algorithms the main difference is the presence of quadratic terms in the mixed variables. In the case of shear deformable beams these terms ensure that the proper finite thickness solution is obtained.

  20. Structural Insights into Calcium-Bound S100P and the V Domain of the RAGE Complex

    Science.gov (United States)

    Penumutchu, Srinivasa R.; Chou, Ruey-Hwang; Yu, Chin

    2014-01-01

    The S100P protein is a member of the S100 family of calcium-binding proteins and possesses both intracellular and extracellular functions. Extracellular S100P binds to the cell surface receptor for advanced glycation end products (RAGE) and activates its downstream signaling cascade to meditate tumor growth, drug resistance and metastasis. Preventing the formation of this S100P-RAGE complex is an effective strategy to treat various disease conditions. Despite its importance, the detailed structural characterization of the S100P-RAGE complex has not yet been reported. In this study, we report that S100P preferentially binds to the V domain of RAGE. Furthermore, we characterized the interactions between the RAGE V domain and Ca2+-bound S100P using various biophysical techniques, including isothermal titration calorimetry (ITC), fluorescence spectroscopy, multidimensional NMR spectroscopy, functional assays and site-directed mutagenesis. The entropy-driven binding between the V domain of RAGE and Ca+2-bound S100P was found to lie in the micromolar range (Kd of ∼6 µM). NMR data-driven HADDOCK modeling revealed the putative sites that interact to yield a proposed heterotetrameric model of the S100P-RAGE V domain complex. Our study on the spatial structural information of the proposed protein-protein complex has pharmaceutical relevance and will significantly contribute toward drug development for the prevention of RAGE-related multifarious diseases. PMID:25084534

  1. Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

    Energy Technology Data Exchange (ETDEWEB)

    Teplova, Marianna; Hafner, Markus; Teplov, Dmitri; Essig, Katharina; Tuschl, Thomas; Patel, Dinshaw J. [MSKCC; (Rockefeller)

    2013-09-27

    Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins.

  2. Structural insights into calcium-bound S100P and the V domain of the RAGE complex.

    Directory of Open Access Journals (Sweden)

    Srinivasa R Penumutchu

    Full Text Available The S100P protein is a member of the S100 family of calcium-binding proteins and possesses both intracellular and extracellular functions. Extracellular S100P binds to the cell surface receptor for advanced glycation end products (RAGE and activates its downstream signaling cascade to meditate tumor growth, drug resistance and metastasis. Preventing the formation of this S100P-RAGE complex is an effective strategy to treat various disease conditions. Despite its importance, the detailed structural characterization of the S100P-RAGE complex has not yet been reported. In this study, we report that S100P preferentially binds to the V domain of RAGE. Furthermore, we characterized the interactions between the RAGE V domain and Ca(2+-bound S100P using various biophysical techniques, including isothermal titration calorimetry (ITC, fluorescence spectroscopy, multidimensional NMR spectroscopy, functional assays and site-directed mutagenesis. The entropy-driven binding between the V domain of RAGE and Ca(+2-bound S100P was found to lie in the micromolar range (Kd of ∼ 6 µM. NMR data-driven HADDOCK modeling revealed the putative sites that interact to yield a proposed heterotetrameric model of the S100P-RAGE V domain complex. Our study on the spatial structural information of the proposed protein-protein complex has pharmaceutical relevance and will significantly contribute toward drug development for the prevention of RAGE-related multifarious diseases.

  3. The DMM Bound

    DEFF Research Database (Denmark)

    Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias

    2010-01-01

    In this paper we derive aggregate separation bounds, named after Davenport-Mahler-Mignotte (DMM), on the isolated roots of polynomial systems, specifically on the minimum distance between any two such roots. The bounds exploit the structure of the system and the height of the sparse (or toric) re...... bound on the number of steps that subdivision-based algorithms perform in order to isolate all real roots of a polynomial system. This leads to the first complexity bound of Milne's algorithm [22] in 2D....

  4. Crystal Structures of Human GlyRα3 Bound to Ivermectin

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Xin; Chen, Hao; Shaffer, Paul L.

    2017-06-01

    Ivermectin acts as a positive allosteric modulator of several Cys-loop receptors including the glutamate-gated chloride channels (GluCls), γ-aminobutyric acid receptors (GABAARs), glycine receptors (GlyRs), and neuronal α7-nicotinic receptors (α7 nAChRs). The crystal structure of Caenorhabditis elegans GluCl complexed with ivermectin revealed the details of its ivermectin binding site. Although the electron microscopy structure of zebrafish GlyRα1 complexed with ivermectin demonstrated a similar binding orientation, detailed structural information on the ivermectin binding and pore opening for Cys-loop receptors in vertebrates has been elusive. Here we present the crystal structures of human GlyRα3 in complex with ivermectin at 2.85 and 3.08 Å resolution. Our structures allow us to explore in detail the molecular recognition of ivermectin by GlyRs, GABAARs, and α7 nAChRs. Comparisons with previous structures reveal how the ivermectin binding expands the ion channel pore. Our results hold promise in structure-based design of GlyR modulators for the treatment of neuropathic pain.

  5. Weak temperature dependence of ageing of structural properties in atomistic model glassformers

    Science.gov (United States)

    Jenkinson, Thomas; Crowther, Peter; Turci, Francesco; Royall, C. Patrick

    2017-08-01

    Ageing phenomena are investigated from a structural perspective in two binary Lennard-Jones glassformers, the Kob-Andersen and Wahnström mixtures. In both, the geometric motif assumed by the glassformer upon supercooling, the locally favoured structure (LFS), has been established. The Kob-Andersen mixture forms bicapped square antiprisms; the Wahnström model forms icosahedra. Upon ageing, we find that the structural relaxation time has a time-dependence consistent with a power law. However, the LFS population and potential energy increase and decrease, respectively, in a logarithmic fashion. Remarkably, over the time scales investigated, which correspond to a factor of 104 change in relaxation times, the rate at which these quantities age appears almost independent of temperature. Only at temperatures far below the Vogel-Fulcher-Tamman temperature do the ageing dynamics slow.

  6. Structure of a rare non-standard sequence k-turn bound by L7Ae protein

    Science.gov (United States)

    Huang, Lin; Lilley, David M.J.

    2014-01-01

    Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates. PMID:24482444

  7. Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA

    Energy Technology Data Exchange (ETDEWEB)

    R Jauch; S Choo; C Ng; P Kolatkar

    2011-12-31

    POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.

  8. Effect of Immersed Wall-Bounded Cylinders on Turbulent Boundary Layer Structure

    Science.gov (United States)

    Zheng, Shaokai; Longmire, Ellen; Hallberg, Michael; Ryan, Mitchell

    2012-11-01

    Single spanwise arrays of wall-mounted cylinders with H/ δ <= 0.2, where H is the cylinder height and δ is the boundary layer thickness, were used to modify turbulent boundary layers (Reτ=2500) in an attempt to affect the organization of the coherent structures in the logarithmic and outer regions. Flow downstream of several array spacings was investigated and compared against an unperturbed case. Instantaneous and averaged velocity fields in streamwise-spanwise planes were obtained by stereo PIV. The PIV cameras and laser sheet optics could be traversed at the local mean flow speed in order to track the evolution of larger structures in the flow. The results are analyzed to determine the streamwise evolution of dominant spanwise modes. Different array spacings are shown to either inhibit or reinforce the organization of vortex packet structures over streamwise distances up to 8 δ. The flying stereo PIV measurements suggest also that dominant structures upstream of the arrays can strongly affect the organization and location of structures downstream. supported by NSF CBET-0933341.

  9. Structure factor of model bidisperse ferrofluids with relatively weak interparticle interactions

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Ekaterina; Pyanzina, Elena; Ivanov, Alexey [Institute of Mathematics, Department of Mathematical Physics, Ural Federal University, Lenin av. 51, 620000 Ekaterinburg (Russian Federation); Minina, Elena [Institute for Computational Physics, Universiät Stuttgart, Allmandring 3, 70569 Stuttgart (Germany); Kantorovich, Sofia, E-mail: sofia.kantorovich@univie.ac.at [Institute of Mathematics, Department of Mathematical Physics, Ural Federal University, Lenin av. 51, 620000 Ekaterinburg (Russian Federation); Faculty of Physics, Computational Physics, University of Vienna, Sensengasse 8, 1090 Vienna (Austria)

    2013-12-14

    In the present manuscript we develop a theoretical approach to describe the pair correlation function of bidisperse magnetic dipolar hard- and soft-spheres. We choose bidisperse system as the first step to allow for polydispersity when studying thermodynamics of magnetic fluids. Using diagram technique we calculate the virial expansion of the pair correlation function up to the first order in density and fourth order in the dipolar strength. Even though, the radial distribution functions are extremely sensitive to the steric potential, we show that the behaviour of the isotropic centre-centre structure factor is almost indifferent to the type of the short-range repulsion. We extensively compare our theoretical results to the data of molecular dynamics simulations, which helps us to understand the range of validity of the virial expansion both on density and magnetic dipolar strength. We also investigate the influence of the granulometric composition on the height, width, and position of the structure factor first peak in order to clarify whether it is possible to extract structural information from experimentally measured small angle neutron scattering intensities.

  10. Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Blaha, Gregor; Stanley, Robin E.; Steitz, Thomas A.; Yale

    2009-10-21

    Elongation factor P (EF-P) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. Here we report the crystal structure of EF-P bound to the Thermus thermophilus 70S ribosome along with the initiator transfer RNA N-formyl-methionyl-tRNAi (fMet-tRNA{sub i}{sup fMet}) and a short piece of messenger RNA (mRNA) at a resolution of 3.5 angstroms. EF-P binds to a site located between the binding site for the peptidyl tRNA (P site) and the exiting tRNA (E site). It spans both ribosomal subunits with its amino-terminal domain positioned adjacent to the aminoacyl acceptor stem and its carboxyl-terminal domain positioned next to the anticodon stem-loop of the P site-bound initiator tRNA. Domain II of EF-P interacts with the ribosomal protein L1, which results in the largest movement of the L1 stalk that has been observed in the absence of ratcheting of the ribosomal subunits. EF-P facilitates the proper positioning of the fMet-tRNA{sub i}{sup fMet} for the formation of the first peptide bond during translation initiation.

  11. Time-Bounded Reachability in Tree-Structured QBDs by Abstraction

    NARCIS (Netherlands)

    Klink, Daniel; Remke, Anne Katharina Ingrid; Haverkort, Boudewijn R.H.M.; Katoen, Joost P.

    This paper studies quantitative model checking of infinite tree-like (continuous-time) Markov chains. These tree-structured quasi-birth death processes are equivalent to probabilistic pushdown automata and recursive Markov chains and are widely used in the field of performance evaluation. We

  12. Time-bounded reachability in tree-structured QBDs by abstraction

    NARCIS (Netherlands)

    Klink, Daniel; Remke, Anne Katharina Ingrid; Haverkort, Boudewijn R.H.M.; Katoen, Joost P.

    This paper studies quantitative model checking of infinite tree-like (continuous-time) Markov chains. These tree-structured quasi-birth death processes are equivalent to probabilistic pushdown automata and recursive Markov chains and are widely used in the field of performance evaluation. We

  13. Estimating Multivariate Exponentail-Affine Term Structure Models from Coupon Bound Prices using Nonlinear Filtering

    DEFF Research Database (Denmark)

    Baadsgaard, Mikkel; Nielsen, Jan Nygaard; Madsen, Henrik

    2000-01-01

    , the central tendency and stochastic volatility. Emphasis is placed on the particular class of exponential-affine term structure models that permits solving the bond pricing PDE in terms of a system of ODEs. It is assumed that coupon bond prices are contaminated by additive white noise, where the stochastic...

  14. Apo- and Cellopentaose-bound Structures of the Bacterial Cellulose Synthase Subunit BcsZ

    Energy Technology Data Exchange (ETDEWEB)

    Mazur, Olga; Zimmer, Jochen (UV)

    2012-10-25

    Cellulose, a very abundant extracellular polysaccharide, is synthesized in a finely tuned process that involves the activity of glycosyl-transferases and hydrolases. The cellulose microfibril consists of bundles of linear {beta}-1,4-glucan chains that are synthesized inside the cell; however, the mechanism by which these polymers traverse the cell membrane is currently unknown. In Gram-negative bacteria, the cellulose synthase complex forms a trans-envelope complex consisting of at least four subunits. Although three of these subunits account for the synthesis and translocation of the polysaccharide, the fourth subunit, BcsZ, is a periplasmic protein with endo-{beta}-1,4-glucanase activity. BcsZ belongs to family eight of glycosyl-hydrolases, and its activity is required for optimal synthesis and membrane translocation of cellulose. In this study we report two crystal structures of BcsZ from Escherichia coli. One structure shows the wild-type enzyme in its apo form, and the second structure is for a catalytically inactive mutant of BcsZ in complex with the substrate cellopentaose. The structures demonstrate that BcsZ adopts an ({alpha}/{alpha}){sub 6}-barrel fold and that it binds four glucan moieties of cellopentaose via highly conserved residues exclusively on the nonreducing side of its catalytic center. Thus, the BcsZ-cellopentaose structure most likely represents a posthydrolysis state in which the newly formed nonreducing end has already left the substrate binding pocket while the enzyme remains attached to the truncated polysaccharide chain. We further show that BcsZ efficiently degrades {beta}-1,4-glucans in in vitro cellulase assays with carboxymethyl-cellulose as substrate.

  15. Crystal Structures of Staphylococcus epidermidis Mevalonate Diphosphate Decarboxylase Bound to Inhibitory Analogs Reveal New Insight into Substrate Binding and Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Barta, Michael L.; Skaff, D. Andrew; McWhorter, William J.; Herdendorf, Timothy J.; Miziorko, Henry M.; Geisbrecht, Brian V. (UMKC)

    2011-10-28

    The polyisoprenoid compound undecaprenyl phosphate is required for biosynthesis of cell wall peptidoglycans in Gram-positive bacteria, including pathogenic Enterococcus, Streptococcus, and Staphylococcus spp. In these organisms, the mevalonate pathway is used to produce the precursor isoprenoid, isopentenyl 5-diphosphate. Mevalonate diphosphate decarboxylase (MDD) catalyzes formation of isopentenyl 5-diphosphate in an ATP-dependent irreversible reaction and is therefore an attractive target for inhibitor development that could lead to new antimicrobial agents. To facilitate exploration of this possibility, we report the crystal structure of Staphylococcus epidermidis MDD (1.85 {angstrom} resolution) and, to the best of our knowledge, the first structures of liganded MDD. These structures include MDD bound to the mevalonate 5-diphosphate analogs diphosphoglycolyl proline (2.05 {angstrom} resolution) and 6-fluoromevalonate diphosphate (FMVAPP; 2.2 {angstrom} resolution). Comparison of these structures provides a physical basis for the significant differences in K{sub i} values observed for these inhibitors. Inspection of enzyme/inhibitor structures identified the side chain of invariant Ser{sup 192} as making potential contributions to catalysis. Significantly, Ser {yields} Ala substitution of this side chain decreases k{sub cat} by {approx}10{sup 3}-fold, even though binding interactions between FMVAPP and this mutant are similar to those observed with wild type MDD, as judged by the 2.1 {angstrom} cocrystal structure of S192A with FMVAPP. Comparison of microbial MDD structures with those of mammalian counterparts reveals potential targets at the active site periphery that may be exploited to selectively target the microbial enzymes. These studies provide a structural basis for previous observations regarding the MDD mechanism and inform future work toward rational inhibitor design.

  16. Structural analysis of a functional DIAP1 fragment bound to grim and hid peptides.

    Science.gov (United States)

    Wu, J W; Cocina, A E; Chai, J; Hay, B A; Shi, Y

    2001-07-01

    The inhibitor of apoptosis protein DIAP1 suppresses apoptosis in Drosophila, with the second BIR domain (BIR2) playing an important role. Three proteins, Hid, Grim, and Reaper, promote apoptosis, in part by binding to DIAP1 through their conserved N-terminal sequences. The crystal structures of DIAP1-BIR2 by itself and in complex with the N-terminal peptides from Hid and Grim reveal that these peptides bind a surface groove on DIAP1, with the first four amino acids mimicking the binding of the Smac tetrapeptide to XIAP. The next 3 residues also contribute to binding through hydrophobic interactions. Interestingly, peptide binding induces the formation of an additional alpha helix in DIAP1. Our study reveals the structural conservation and diversity necessary for the binding of IAPs by the Drosophila Hid/Grim/Reaper and the mammalian Smac proteins.

  17. Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane

    Energy Technology Data Exchange (ETDEWEB)

    Lieberman, R.L.; Rosenzweig, A.C. (NWU)

    2010-03-08

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. We have determined the structure of pMMO from the methanotroph Methylococcus capsulatus (Bath) to a resolution of 2.8 {angstrom}. The enzyme is a trimer with an {alpha}{sub 3}{beta}{sub 3}{gamma}{sub 3} polypeptide arrangement. Two metal centres, modelled as mononuclear copper and dinuclear copper, are located in soluble regions of each pmoB subunit, which resembles cytochrome c oxidase subunit II. A third metal centre, occupied by zinc in the crystal, is located within the membrane. The structure provides new insight into the molecular details of biological methane oxidation.

  18. A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity

    OpenAIRE

    Takao, Haruna; Hirabayashi, Kei; Nishigaya, Yuki; Kouriki, Haruna; Nakaniwa, Tetsuko; Hagiwara, Yoshinori; Harada, Jiro; Sato, Hideaki; Yamazaki, Toshimasa; Sakakibara, Yoichi; Suiko, Masahito; Asada, Yujiro; Takahashi, Yasuhiro; Yamamoto, Ken; Fukuyama, Keiichi

    2017-01-01

    Biliverdin reductase catalyses the last step in haem degradation and produces the major lipophilic antioxidant bilirubin via reduction of biliverdin, using NAD(P)H as a cofactor. Despite the importance of biliverdin reductase in maintaining the redox balance, the molecular details of the reaction it catalyses remain unknown. Here we present the crystal structure of biliverdin reductase in complex with biliverdin and NADP+. Unexpectedly, two biliverdin molecules, which we designated the proxim...

  19. Orthogonal Range Reporting: Query Lower Bounds, Optimal Structures in 3-d, and Higher Dimensional Improvements

    DEFF Research Database (Denmark)

    Afshani, Peyman; Arge, Lars Allan; Larsen, Kasper Dalgaard

    2010-01-01

    , this is not the case in higher dimensions. In this paper we provide a space optimal pointer machine data structure for 3-d orthogonal range reporting that answers queries in O(log n + k) time. Thus we settle the complexity of the problem in 3-d. We use this result to obtain improved structures in higher dimensions...... data structure for the d-dimensional orthogonal range reporting problem in the pointer machine model of computation that uses S(n) space must spend Ω((log n/ log(S(n)/n))⌊d/2⌋--1) time to answer queries. Thus, if S(n)/n is poly-logarithmic, then the query time is at least Ω((log n/ log log n)⌊d/2......Orthogonal range reporting is the problem of storing a set of n points in d-dimensional space, such that the k points in an axis-orthogonal query box can be reported efficiently. While the 2-d version of the problem was completely characterized in the pointer machine model more than two decades ago...

  20. Deterioration Models for Cement Bound Materials in Structural Design and Evaluation of Heavy Duty Pavements

    DEFF Research Database (Denmark)

    Skar, Asmus; Holst, Mogens Løvendorf

    Ports and industries require special types of pavements to resist the heavy static load from containers and continuous loads from operation vehicles. To reduce the risk of rutting and settlements over time concrete or compositepavement systems are typically applied. The structural design of such ......Ports and industries require special types of pavements to resist the heavy static load from containers and continuous loads from operation vehicles. To reduce the risk of rutting and settlements over time concrete or compositepavement systems are typically applied. The structural design...... of such pavements are today based on Mechanistic-Empirical (M-E) methods. The M-E method is appropriate for many situations, in other situations it may lead to overdesign, or maybe worse, underdesign. The method has limited capabilities and cannot account for signicant factors affecting the pavement response...... number of model parameters. In order to move a step towards more generalised structural design methods for analysis of heavy duty pavements, this study aims at developing a mechanistic approach based on constitutive models. A simple framework for engineering application is sought; creating a rational...

  1. Crystal structure of the[mu]-opioid receptor bound to a morphinan antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Mathiesen, Jesper M.; Sunahara, Roger K.; Pardo, Leonardo; Weis, William I.; Kobilka, Brian K.; Granier, Sébastien (Michigan-Med); (Stanford-MED); (UAB, Spain)

    2012-06-27

    Opium is one of the world's oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnoea and dependence) by binding to and activating the G-protein-coupled {mu}-opioid receptor ({mu}-OR) in the central nervous system. Here we describe the 2.8 {angstrom} crystal structure of the mouse {mu}-OR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket observed in most G-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the {mu}-OR crystallizes as a two-fold symmetrical dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.

  2. Structure of HIV-1 Reverse Transcriptase with the Inhibitor -thujaplicinol Bound at the RNase H Active Site

    Energy Technology Data Exchange (ETDEWEB)

    Himmel, D.; Maegley, K; Pauly, T; Bauman, J; Das, K; Dharia, C; Clark, Jr., A; Ryan, K; Hickey, M; et al.

    2009-01-01

    Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. Inhibitors that act against new targets, such as RNH, should be effective against all of the current drug-resistant variants. Here, we present 2.80 {angstrom} and 2.04 {angstrom} resolution crystal structures of an RNH inhibitor, {beta}-thujaplicinol, bound at the RNH active site of both HIV-1 RT and an isolated RNH domain. {beta}-thujaplicinol chelates two divalent metal ions at the RNH active site. We provide biochemical evidence that {beta}-thujaplicinol is a slow-binding RNH inhibitor with noncompetitive kinetics and suggest that it forms a tropylium ion that interacts favorably with RT and the RNA:DNA substrate.

  3. Nuclear structure properties and stellar weak rates for 76Se: Unblocking of the Gamow Teller strength

    Science.gov (United States)

    Nabi, Jameel-Un; Ishfaq, Mavra; Böyükata, Mahmut; Riaz, Muhammad

    2017-10-01

    At finite temperatures (≥ 107K), 76Se is abundant in the core of massive stars and electron capture on 76Se has a consequential role to play in the dynamics of core-collapse. The present work may be classified into two main categories. In the first phase we study the nuclear structure properties of 76Se using the interacting boson model-1 (IBM-1). The IBM-1 investigations include the energy levels, B (E 2) values and the prediction of the geometry. We performed the extended consistent-Q formalism (ECQF) calculation and later the triaxial formalism calculation (constructed by adding the cubic term to the ECQF). The geometry of 76Se can be envisioned within the formalism of the potential energy surface based on the classical limit of IBM-1 model. In the second phase, we reconfirm the unblocking of the Gamow-Teller (GT) strength in 76Se (a test case for nuclei having N > 40 and Z data and previous calculations. The calculated GT distribution fulfills the Ikeda sum rule. Rates for β-delayed neutrons and emission probabilities are also calculated. Our study suggests that at high stellar temperatures and low densities, the β+-decay on 76Se should not be neglected and needs to be taken into consideration along with electron capture rates for simulation of presupernova evolution of massive stars.

  4. Structural, optical and weak magnetic properties of Co and Mn codoped TiO2 nanoparticles

    Science.gov (United States)

    Kumar, Anand; Kashyap, Manish K.; Sabharwal, Namita; Kumar, Sarvesh; Kumar, Ashok; Kumar, Parmod; Asokan, K.

    2017-11-01

    The present investigation focuses on the structural properties and magnetic response of Co, Mn and Co-Mn doped TiO2 nanoparticles (within 3% dilute doping) along with their optical and electrical studies. X-ray diffraction (XRD) patterns for all these samples show the formation of tetragonal TiO2 anatase phase with no extra impurity phases. Further, Raman bands at 143 cm-1, 396 cm-1, 516 cm-1 and 639 cm-1 also confirm the anatase phase in these samples. Diamagnetic response has been observed in pure TiO2 nanoparticles. However, room temperature (RT) ferromagnetism has been observed with Co and/or Mn doping which gets enhanced further with codoping of Co ions. The observed ferromagnetism has been attributed to the formation of shallow levels with doping/codoping. The Co and/or Mn-doped TiO2 nanoparticles are referred as diluted magnetic semiconductors due to their combined semiconducting and ferromagnetic response. UV-Vis spectra show the band gap of these samples are in the range of 3.03 eV-3.24 eV and a reduction in band gap is observed after codoping. The temperature dependent electrical conductivity measurements also show an enhancement in conductivity after codoping at RT.

  5. Structure of promoter-bound TFIID and insight into human PIC assembly

    Science.gov (United States)

    Louder, Robert K.; He, Yuan; López-Blanco, José Ramón; Fang, Jie; Chacón, Pablo; Nogales, Eva

    2016-01-01

    The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy (cryo-EM) at sub-nanometer resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-EM reconstruction of a fully-assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation. PMID:27007846

  6. Structure of IL-22 Bound to Its High-Affinity IL-22R1 Chain

    Energy Technology Data Exchange (ETDEWEB)

    Jones, B.C.; Logsdon, N.J.; Walter, M.R. (UAB)

    2008-09-29

    IL-22 is an IL-10 family cytokine that initiates innate immune responses against bacterial pathogens and contributes to immune disease. IL-22 biological activity is initiated by binding to a cell-surface complex composed of IL-22R1 and IL-10R2 receptor chains and further regulated by interactions with a soluble binding protein, IL-22BP, which shares sequence similarity with an extracellular region of IL-22R1 (sIL-22R1). IL-22R1 also pairs with the IL-20R2 chain to induce IL-20 and IL-24 signaling. To define the molecular basis of these diverse interactions, we have determined the structure of the IL-22/sIL-22R1 complex. The structure, combined with homology modeling and surface plasmon resonance studies, defines the molecular basis for the distinct affinities and specificities of IL-22 and IL-10 receptor chains that regulate cellular targeting and signal transduction to elicit effective immune responses.

  7. Bounded Rationality

    National Research Council Canada - National Science Library

    Ballester Pla, Coralio; Hernández, Penélope

    2012-01-01

    The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models...

  8. Bounding the $\

    CERN Document Server

    Gutiérrez-Rodríguez, A

    2003-01-01

    A bound on the nu /sup tau / magnetic moment is calculated through the reaction e/sup +/e/sup -/ to nu nu gamma at the Z/sub 1/-pole, and in the framework of a left-right symmetric model at LEP energies. We find that the bound is almost independent of the mixing angle phi of the model in the allowed experimental range for this parameter. (31 refs).

  9. A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity.

    Science.gov (United States)

    Takao, Haruna; Hirabayashi, Kei; Nishigaya, Yuki; Kouriki, Haruna; Nakaniwa, Tetsuko; Hagiwara, Yoshinori; Harada, Jiro; Sato, Hideaki; Yamazaki, Toshimasa; Sakakibara, Yoichi; Suiko, Masahito; Asada, Yujiro; Takahashi, Yasuhiro; Yamamoto, Ken; Fukuyama, Keiichi; Sugishima, Masakazu; Wada, Kei

    2017-02-07

    Biliverdin reductase catalyses the last step in haem degradation and produces the major lipophilic antioxidant bilirubin via reduction of biliverdin, using NAD(P)H as a cofactor. Despite the importance of biliverdin reductase in maintaining the redox balance, the molecular details of the reaction it catalyses remain unknown. Here we present the crystal structure of biliverdin reductase in complex with biliverdin and NADP+. Unexpectedly, two biliverdin molecules, which we designated the proximal and distal biliverdins, bind with stacked geometry in the active site. The nicotinamide ring of the NADP+ is located close to the reaction site on the proximal biliverdin, supporting that the hydride directly attacks this position of the proximal biliverdin. The results of mutagenesis studies suggest that a conserved Arg185 is essential for the catalysis. The distal biliverdin probably acts as a conduit to deliver the proton from Arg185 to the proximal biliverdin, thus yielding bilirubin.

  10. Structure analysis of the membrane-bound dermcidin-derived peptide SSL-25 from human sweat.

    Science.gov (United States)

    Mühlhäuser, Philipp; Wadhwani, Parvesh; Strandberg, Erik; Bürck, Jochen; Ulrich, Anne S

    2017-12-01

    SSL-25 (SSLLEKGLDGAKKAVGGLGKLGKDA) is one of the shortest peptides present in human sweat and is produced after the proteolytic processing of the parent peptide dermcidin. Both peptides are reported to have antimicrobial function. To determine the structure of SSL-25 in lipid bilayers, a series of 19 F-labeled SSL-25 analogs were synthesized. Circular dichroism (CD) analysis showed that SSL-25 and all of its analogs formed α-helices in the presence of lipid vesicles, thus allowing a detailed analysis via oriented CD and solid-state NMR. The results suggest that SSL-25 resides on the membrane surface with a slight helix tilt angle. A detailed 19 F NMR analysis revealed that SSL-25 does not form a continuous helix. The α-helical structure of the N-terminal part of the peptide was preserved in membranes of different lipid compositions and at various peptide-to-lipid molar ratios, but the C-terminus was disordered and did not fold into a well-defined α-helical conformation. Furthermore, the NMR results showed that SSL-25 resides on the membrane surface and does not re-orient into the membrane in response to changes in either peptide concentration or membrane composition. SSL-25 does not aggregate and remains fully mobile within the membrane bilayer, as shown by 19 F NMR. SSL-25 has a high binding affinity toward bilayers mimicking bacterial lipid compositions, but does not bind to mammalian model membranes containing cholesterol. These observations may explain the selectivity of this peptide for bacterial membranes, and they are also in line with basic biophysical considerations on spontaneous lipid curvature and the general effect of cholesterol on peptide/lipid interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Structure of RNA 3′-phosphate cyclase bound to substrate RNA

    Science.gov (United States)

    Desai, Kevin K.; Bingman, Craig A.; Cheng, Chin L.; Phillips, George N.

    2014-01-01

    RNA 3′-phosphate cyclase (RtcA) catalyzes the ATP-dependent cyclization of a 3′-phosphate to form a 2′,3′-cyclic phosphate at RNA termini. Cyclization proceeds through RtcA–AMP and RNA(3′)pp(5′)A covalent intermediates, which are analogous to intermediates formed during catalysis by the tRNA ligase RtcB. Here we present a crystal structure of Pyrococcus horikoshii RtcA in complex with a 3′-phosphate terminated RNA and adenosine in the AMP-binding pocket. Our data reveal that RtcA recognizes substrate RNA by ensuring that the terminal 3′-phosphate makes a large contribution to RNA binding. Furthermore, the RNA 3′-phosphate is poised for in-line attack on the P–N bond that links the phosphorous atom of AMP to Nε of His307. Thus, we provide the first insights into RNA 3′-phosphate termini recognition and the mechanism of 3′-phosphate activation by an Rtc enzyme. PMID:25161314

  12. Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering.

    Science.gov (United States)

    Chang, Jinyuan; Zhou, Wen; Zhou, Wen-Xin; Wang, Lan

    2017-03-01

    Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence, the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and are available on CRAN. © 2016, The International Biometric Society.

  13. The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Vincenzo A.; Shepherd, Sharon M.; English, Grant; Coulthurst, Sarah J.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

    2011-12-01

    The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein–protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners.

  14. Structure of Gαi1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange

    OpenAIRE

    Johnston, Christopher A.; Willard, Francis S.; Jezyk, Mark R.; Fredericks, Zoey; Bodor, Erik T.; Jones, Miller B.; Blaesius, Rainer; Watts, Val J.; Harden, T. Kendall; Sondek, John; Ramer, J. Kevin; Siderovski, David P.

    2005-01-01

    Heterotrimeric G-proteins are molecular switches that regulate numerous signaling pathways involved in cellular physiology. This characteristic is achieved by the adoption of two principal states: an inactive, GDP-bound and an active, GTP-bound state. Under basal conditions G-proteins exist in the inactive GDP-bound state, thus nucleotide exchange is crucial to the onset of signaling. Despite our understanding of G-protein signaling pathways, the mechanism of nucleotide exchange remains elusi...

  15. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle.

    Science.gov (United States)

    Schneider, Bohdan; Božíková, Paulína; Čech, Petr; Svozil, Daniel; Černý, Jiří

    2017-10-18

    We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes.

  16. Search for weakly decaying $\\overline{\\Lambda\\mathrm{n}}$ and $\\Lambda\\Lambda $ exotic bound states in central Pb-Pb collisions at $\\sqrt{s_{\\rm NN}}$ = 2.76 TeV

    CERN Document Server

    Adam, Jaroslav; Aggarwal, Madan Mohan; Aglieri Rinella, Gianluca; Agnello, Michelangelo; Agrawal, Neelima; Ahammed, Zubayer; Ahmed, Ijaz; Ahn, Sang Un; Aimo, Ilaria; Aiola, Salvatore; Ajaz, Muhammad; Akindinov, Alexander; Alam, Sk Noor; Aleksandrov, Dmitry; Alessandro, Bruno; Alexandre, Didier; Alfaro Molina, Jose Ruben; Alici, Andrea; Alkin, Anton; Alme, Johan; Alt, Torsten; Altinpinar, Sedat; Altsybeev, Igor; Alves Garcia Prado, Caio; Andrei, Cristian; Andronic, Anton; Anguelov, Venelin; Anielski, Jonas; Anticic, Tome; Antinori, Federico; Antonioli, Pietro; Aphecetche, Laurent Bernard; Appelshaeuser, Harald; Arcelli, Silvia; Armesto Perez, Nestor; Arnaldi, Roberta; Aronsson, Tomas; Arsene, Ionut Cristian; Arslandok, Mesut; Augustinus, Andre; Averbeck, Ralf Peter; Azmi, Mohd Danish; Bach, Matthias Jakob; Badala, Angela; Baek, Yong Wook; Bagnasco, Stefano; Bailhache, Raphaelle Marie; Bala, Renu; Baldisseri, Alberto; Ball, Markus; Baltasar Dos Santos Pedrosa, Fernando; Baral, Rama Chandra; Barbano, Anastasia Maria; Barbera, Roberto; Barile, Francesco; Barnafoldi, Gergely Gabor; Barnby, Lee Stuart; Ramillien Barret, Valerie; Bartalini, Paolo; Bartke, Jerzy Gustaw; Bartsch, Esther; Basile, Maurizio; Bastid, Nicole; Basu, Sumit; Bathen, Bastian; Batigne, Guillaume; Batista Camejo, Arianna; Batyunya, Boris; Batzing, Paul Christoph; Bearden, Ian Gardner; Beck, Hans; Bedda, Cristina; Behera, Nirbhay Kumar; Belikov, Iouri; Bellini, Francesca; Bello Martinez, Hector; Bellwied, Rene; Belmont Iii, Ronald John; Belmont Moreno, Ernesto; Belyaev, Vladimir; Bencedi, Gyula; Beole, Stefania; Berceanu, Ionela; Bercuci, Alexandru; Berdnikov, Yaroslav; Berenyi, Daniel; Bertens, Redmer Alexander; Berzano, Dario; Betev, Latchezar; Bhasin, Anju; Bhat, Inayat Rasool; Bhati, Ashok Kumar; Bhattacharjee, Buddhadeb; Bhom, Jihyun; Bianchi, Livio; Bianchi, Nicola; Bianchin, Chiara; Bielcik, Jaroslav; Bielcikova, Jana; Bilandzic, Ante; Biswas, Saikat; Bjelogrlic, Sandro; Blanco, Fernando; Blau, Dmitry; Blume, Christoph; Bock, Friederike; Bogdanov, Alexey; Boggild, Hans; Boldizsar, Laszlo; Bombara, Marek; Book, Julian Heinz; Borel, Herve; Borissov, Alexander; Borri, Marcello; Bossu, Francesco; Botje, Michiel; Botta, Elena; Boettger, Stefan; Braun-Munzinger, Peter; Bregant, Marco; Breitner, Timo Gunther; Broker, Theo Alexander; Browning, Tyler Allen; Broz, Michal; Brucken, Erik Jens; Bruna, Elena; Bruno, Giuseppe Eugenio; Budnikov, Dmitry; Buesching, Henner; Bufalino, Stefania; Buncic, Predrag; Busch, Oliver; Buthelezi, Edith Zinhle; Buxton, Jesse Thomas; Caffarri, Davide; Cai, Xu; Caines, Helen Louise; Calero Diaz, Liliet; Caliva, Alberto; Calvo Villar, Ernesto; Camerini, Paolo; Carena, Francesco; Carena, Wisla; Castillo Castellanos, Javier Ernesto; Castro, Andrew John; Casula, Ester Anna Rita; Cavicchioli, Costanza; Ceballos Sanchez, Cesar; Cepila, Jan; Cerello, Piergiorgio; Chang, Beomsu; Chapeland, Sylvain; Chartier, Marielle; Charvet, Jean-Luc Fernand; Chattopadhyay, Subhasis; Chattopadhyay, Sukalyan; Chelnokov, Volodymyr; Cherney, Michael Gerard; Cheshkov, Cvetan Valeriev; Cheynis, Brigitte; Chibante Barroso, Vasco Miguel; Dobrigkeit Chinellato, David; Chochula, Peter; Choi, Kyungeon; Chojnacki, Marek; Choudhury, Subikash; Christakoglou, Panagiotis; Christensen, Christian Holm; Christiansen, Peter; Chujo, Tatsuya; Chung, Suh-Urk; Cicalo, Corrado; Cifarelli, Luisa; Cindolo, Federico; Cleymans, Jean Willy Andre; Colamaria, Fabio Filippo; Colella, Domenico; Collu, Alberto; Colocci, Manuel; Conesa Balbastre, Gustavo; Conesa Del Valle, Zaida; Connors, Megan Elizabeth; Contreras Nuno, Jesus Guillermo; Cormier, Thomas Michael; Corrales Morales, Yasser; Cortes Maldonado, Ismael; Cortese, Pietro; Cosentino, Mauro Rogerio; Costa, Filippo; Crochet, Philippe; Cruz Albino, Rigoberto; Cuautle Flores, Eleazar; Cunqueiro Mendez, Leticia; Dahms, Torsten; Dainese, Andrea; Danu, Andrea; Das, Debasish; Das, Indranil; Das, Supriya; Dash, Ajay Kumar; Dash, Sadhana; De, Sudipan; De Caro, Annalisa; De Cataldo, Giacinto; De Cuveland, Jan; De Falco, Alessandro; De Gruttola, Daniele; De Marco, Nora; De Pasquale, Salvatore; Deisting, Alexander; Deloff, Andrzej; Denes, Ervin Sandor; D'Erasmo, Ginevra; Di Bari, Domenico; Di Mauro, Antonio; Di Nezza, Pasquale; Diaz Corchero, Miguel Angel; Dietel, Thomas; Dillenseger, Pascal; Divia, Roberto; Djuvsland, Oeystein; Dobrin, Alexandru Florin; Dobrowolski, Tadeusz Antoni; Domenicis Gimenez, Diogenes; Donigus, Benjamin; Dordic, Olja; Dubey, Anand Kumar; Dubla, Andrea; Ducroux, Laurent; Dupieux, Pascal; Ehlers Iii, Raymond James; Elia, Domenico; Engel, Heiko; Erazmus, Barbara Ewa; Erhardt, Filip; Eschweiler, Dominic; Espagnon, Bruno; Estienne, Magali Danielle; Esumi, Shinichi; Evans, David; Evdokimov, Sergey; Eyyubova, Gyulnara; Fabbietti, Laura; Fabris, Daniela; Faivre, Julien; Fantoni, Alessandra; Fasel, Markus; Feldkamp, Linus; Felea, Daniel; Feliciello, Alessandro; Feofilov, Grigorii; Ferencei, Jozef; Fernandez Tellez, Arturo; Gonzalez Ferreiro, Elena; Ferretti, Alessandro; Festanti, Andrea; Figiel, Jan; Araujo Silva Figueredo, Marcel; Filchagin, Sergey; Finogeev, Dmitry; Fionda, Fiorella; Fiore, Enrichetta Maria; Fleck, Martin Gabriel; Floris, Michele; Foertsch, Siegfried Valentin; Foka, Panagiota; Fokin, Sergey; Fragiacomo, Enrico; Francescon, Andrea; Frankenfeld, Ulrich Michael; Fuchs, Ulrich; Furget, Christophe; Furs, Artur; Fusco Girard, Mario; Gaardhoeje, Jens Joergen; Gagliardi, Martino; Gago Medina, Alberto Martin; Gallio, Mauro; Gangadharan, Dhevan Raja; Ganoti, Paraskevi; Gao, Chaosong; Garabatos Cuadrado, Jose; Garcia-Solis, Edmundo Javier; Gargiulo, Corrado; Gasik, Piotr Jan; Germain, Marie; Gheata, Andrei George; Gheata, Mihaela; Ghosh, Premomoy; Ghosh, Sanjay Kumar; Gianotti, Paola; Giubellino, Paolo; Giubilato, Piero; Gladysz-Dziadus, Ewa; Glassel, Peter; Gomez Ramirez, Andres; Gonzalez Zamora, Pedro; Gorbunov, Sergey; Gorlich, Lidia Maria; Gotovac, Sven; Grabski, Varlen; Graczykowski, Lukasz Kamil; Grelli, Alessandro; Grigoras, Alina Gabriela; Grigoras, Costin; Grigoryev, Vladislav; Grigoryan, Ara; Grigoryan, Smbat; Grynyov, Borys; Grion, Nevio; Grosse-Oetringhaus, Jan Fiete; Grossiord, Jean-Yves; Grosso, Raffaele; Guber, Fedor; Guernane, Rachid; Guerzoni, Barbara; Gulbrandsen, Kristjan Herlache; Gulkanyan, Hrant; Gunji, Taku; Gupta, Anik; Gupta, Ramni; Haake, Rudiger; Haaland, Oystein Senneset; Hadjidakis, Cynthia Marie; Haiduc, Maria; Hamagaki, Hideki; Hamar, Gergoe; Hanratty, Luke David; Hansen, Alexander; Harris, John William; Hartmann, Helvi; Harton, Austin Vincent; Hatzifotiadou, Despina; Hayashi, Shinichi; Heckel, Stefan Thomas; Heide, Markus Ansgar; Helstrup, Haavard; Herghelegiu, Andrei Ionut; Herrera Corral, Gerardo Antonio; Hess, Benjamin Andreas; Hetland, Kristin Fanebust; Hilden, Timo Eero; Hillemanns, Hartmut; Hippolyte, Boris; Hristov, Peter Zahariev; Huang, Meidana; Humanic, Thomas; Hussain, Nur; Hussain, Tahir; Hutter, Dirk; Hwang, Dae Sung; Ilkaev, Radiy; Ilkiv, Iryna; Inaba, Motoi; Ionita, Costin; Ippolitov, Mikhail; Irfan, Muhammad; Ivanov, Marian; Ivanov, Vladimir; Izucheev, Vladimir; Jacholkowski, Adam Wlodzimierz; Jacobs, Peter Martin; Jahnke, Cristiane; Jang, Haeng Jin; Janik, Malgorzata Anna; Pahula Hewage, Sandun; Jena, Chitrasen; Jena, Satyajit; Jimenez Bustamante, Raul Tonatiuh; Jones, Peter Graham; Jung, Hyungtaik; Jusko, Anton; Kalinak, Peter; Kalweit, Alexander Philipp; Kamin, Jason Adrian; Kang, Ju Hwan; Kaplin, Vladimir; Kar, Somnath; Karasu Uysal, Ayben; Karavichev, Oleg; Karavicheva, Tatiana; Karpechev, Evgeny; Kebschull, Udo Wolfgang; Keidel, Ralf; Keijdener, Darius Laurens; Keil, Markus; Khan, Kamal; Khan, Mohammed Mohisin; Khan, Palash; Khan, Shuaib Ahmad; Khanzadeev, Alexei; Kharlov, Yury; Kileng, Bjarte; Kim, Beomkyu; Kim, Do Won; Kim, Dong Jo; Kim, Hyeonjoong; Kim, Jinsook; Kim, Mimae; Kim, Minwoo; Kim, Se Yong; Kim, Taesoo; Kirsch, Stefan; Kisel, Ivan; Kiselev, Sergey; Kisiel, Adam Ryszard; Kiss, Gabor; Klay, Jennifer Lynn; Klein, Carsten; Klein, Jochen; Klein-Boesing, Christian; Kluge, Alexander; Knichel, Michael Linus; Knospe, Anders Garritt; Kobayashi, Taiyo; Kobdaj, Chinorat; Kofarago, Monika; Kohler, Markus Konrad; Kollegger, Thorsten; Kolozhvari, Anatoly; Kondratev, Valerii; Kondratyeva, Natalia; Kondratyuk, Evgeny; Konevskikh, Artem; Kouzinopoulos, Charalampos; Kovalenko, Vladimir; Kowalski, Marek; Kox, Serge; Koyithatta Meethaleveedu, Greeshma; Kral, Jiri; Kralik, Ivan; Kravcakova, Adela; Krelina, Michal; Kretz, Matthias; Krivda, Marian; Krizek, Filip; Kryshen, Evgeny; Krzewicki, Mikolaj; Kubera, Andrew Michael; Kucera, Vit; Kucheryaev, Yury; Kugathasan, Thanushan; Kuhn, Christian Claude; Kuijer, Paulus Gerardus; Kulakov, Igor; Kumar, Jitendra; Lokesh, Kumar; Kurashvili, Podist; Kurepin, Alexander; Kurepin, Alexey; Kuryakin, Alexey; Kushpil, Svetlana; Kweon, Min Jung; Kwon, Youngil; La Pointe, Sarah Louise; La Rocca, Paola; Lagana Fernandes, Caio; Lakomov, Igor; Langoy, Rune; Lara Martinez, Camilo Ernesto; Lardeux, Antoine Xavier; Lattuca, Alessandra; Laudi, Elisa; Lea, Ramona; Leardini, Lucia; Lee, Graham Richard; Lee, Seongjoo; Legrand, Iosif; Lehnert, Joerg Walter; Lemmon, Roy Crawford; Lenti, Vito; Leogrande, Emilia; Leon Monzon, Ildefonso; Leoncino, Marco; Levai, Peter; Li, Shuang; Li, Xiaomei; Lien, Jorgen Andre; Lietava, Roman; Lindal, Svein; Lindenstruth, Volker; Lippmann, Christian; Lisa, Michael Annan; Ljunggren, Hans Martin; Lodato, Davide Francesco; Lonne, Per-Ivar; Loggins, Vera Renee; Loginov, Vitaly; Loizides, Constantinos; Lopez, Xavier Bernard; Lopez Torres, Ernesto; Lowe, Andrew John; Lu, Xianguo; Luettig, Philipp Johannes; Lunardon, Marcello; Luparello, Grazia; Maevskaya, Alla; Mager, Magnus; Mahajan, Sanjay; Mahmood, Sohail Musa; Maire, Antonin; Majka, Richard Daniel; Malaev, Mikhail; Maldonado Cervantes, Ivonne Alicia; Malinina, Liudmila; Mal'Kevich, Dmitry; Malzacher, Peter; Mamonov, Alexander; Manceau, Loic Henri Antoine; Manko, Vladislav; Manso, Franck; Manzari, Vito; Marchisone, Massimiliano; Mares, Jiri; Margagliotti, Giacomo Vito; Margotti, Anselmo; Margutti, Jacopo; Marin, Ana Maria; Markert, Christina; Marquard, Marco; Martashvili, Irakli; Martin, Nicole Alice; Martin Blanco, Javier; Martinengo, Paolo; Martinez Hernandez, Mario Ivan; Martinez-Garcia, Gines; Martinez Pedreira, Miguel; Martynov, Yevgen; Mas, Alexis Jean-Michel; Masciocchi, Silvia; Masera, Massimo; Masoni, Alberto; Massacrier, Laure Marie; Mastroserio, Annalisa; Matyja, Adam Tomasz; Mayer, Christoph; Mazer, Joel Anthony; Mazzoni, Alessandra Maria; Mcdonald, Daniel; Meddi, Franco; Menchaca-Rocha, Arturo Alejandro; Meninno, Elisa; Mercado-Perez, Jorge; Meres, Michal; Miake, Yasuo; Mieskolainen, Matti Mikael; Mikhaylov, Konstantin; Milano, Leonardo; Milosevic, Jovan; Minervini, Lazzaro Manlio; Mischke, Andre; Mishra, Aditya Nath; Miskowiec, Dariusz Czeslaw; Mitra, Jubin; Mitu, Ciprian Mihai; Mohammadi, Naghmeh; Mohanty, Bedangadas; Molnar, Levente; Montano Zetina, Luis Manuel; Montes Prado, Esther; Morando, Maurizio; Moretto, Sandra; Morreale, Astrid; Morsch, Andreas; Muccifora, Valeria; Mudnic, Eugen; Muhlheim, Daniel Michael; Muhuri, Sanjib; Mukherjee, Maitreyee; Muller, Hans; Mulligan, James Declan; Gameiro Munhoz, Marcelo; Murray, Sean; Musa, Luciano; Musinsky, Jan; Nandi, Basanta Kumar; Nania, Rosario; Nappi, Eugenio; Naru, Muhammad Umair; Nattrass, Christine; Nayak, Kishora; Nayak, Tapan Kumar; Nazarenko, Sergey; Nedosekin, Alexander; Nellen, Lukas; Ng, Fabian; Nicassio, Maria; Niculescu, Mihai; Niedziela, Jeremi; Nielsen, Borge Svane; Nikolaev, Sergey; Nikulin, Sergey; Nikulin, Vladimir; Noferini, Francesco; Nomokonov, Petr; Nooren, Gerardus; Norman, Jaime; Nyanin, Alexander; Nystrand, Joakim Ingemar; Oeschler, Helmut Oskar; Oh, Saehanseul; Oh, Sun Kun; Ohlson, Alice Elisabeth; Okatan, Ali; Okubo, Tsubasa; Olah, Laszlo; Oleniacz, Janusz; Oliveira Da Silva, Antonio Carlos; Oliver, Michael Henry; Onderwaater, Jacobus; Oppedisano, Chiara; Ortiz Velasquez, Antonio; Oskarsson, Anders Nils Erik; Otwinowski, Jacek Tomasz; Oyama, Ken; Ozdemir, Mahmut; Pachmayer, Yvonne Chiara; Pagano, Paola; Paic, Guy; Pajares Vales, Carlos; Pal, Susanta Kumar; Pan, Jinjin; Pandey, Ashutosh Kumar; Pant, Divyash; Papikyan, Vardanush; Pappalardo, Giuseppe; Pareek, Pooja; Park, Woojin; Parmar, Sonia; Passfeld, Annika; Paticchio, Vincenzo; Paul, Biswarup; Pawlak, Tomasz Jan; Peitzmann, Thomas; Pereira Da Costa, Hugo Denis Antonio; Pereira De Oliveira Filho, Elienos; Peresunko, Dmitry Yurevich; Perez Lara, Carlos Eugenio; Peskov, Vladimir; Pestov, Yury; Petracek, Vojtech; Petrov, Viacheslav; Petrovici, Mihai; Petta, Catia; Piano, Stefano; Pikna, Miroslav; Pillot, Philippe; Pinazza, Ombretta; Pinsky, Lawrence; Piyarathna, Danthasinghe; Ploskon, Mateusz Andrzej; Planinic, Mirko; Pluta, Jan Marian; Pochybova, Sona; Podesta Lerma, Pedro Luis Manuel; Poghosyan, Martin; Polishchuk, Boris; Poljak, Nikola; Poonsawat, Wanchaloem; Pop, Amalia; Porteboeuf, Sarah Julie; Porter, R Jefferson; Pospisil, Jan; Prasad, Sidharth Kumar; Preghenella, Roberto; Prino, Francesco; Pruneau, Claude Andre; Pshenichnov, Igor; Puccio, Maximiliano; Puddu, Giovanna; Pujahari, Prabhat Ranjan; Punin, Valery; Putschke, Jorn Henning; Qvigstad, Henrik; Rachevski, Alexandre; Raha, Sibaji; Rajput, Sonia; Rak, Jan; Rakotozafindrabe, Andry Malala; Ramello, Luciano; Raniwala, Rashmi; Raniwala, Sudhir; Rasanen, Sami Sakari; Rascanu, Bogdan Theodor; Rathee, Deepika; Razazi, Vahedeh; Read, Kenneth Francis; Real, Jean-Sebastien; Redlich, Krzysztof; Reed, Rosi Jan; Rehman, Attiq Ur; Reichelt, Patrick Simon; Reicher, Martijn; Reidt, Felix; Ren, Xiaowen; Renfordt, Rainer Arno Ernst; Reolon, Anna Rita; Reshetin, Andrey; Rettig, Felix Vincenz; Revol, Jean-Pierre; Reygers, Klaus Johannes; Riabov, Viktor; Ricci, Renato Angelo; Richert, Tuva Ora Herenui; Richter, Matthias Rudolph; Riedler, Petra; Riegler, Werner; Riggi, Francesco; Ristea, Catalin-Lucian; Rivetti, Angelo; Rocco, Elena; Rodriguez Cahuantzi, Mario; Rodriguez Manso, Alis; Roeed, Ketil; Rogochaya, Elena; Rohr, David Michael; Roehrich, Dieter; Romita, Rosa; Ronchetti, Federico; Ronflette, Lucile; Rosnet, Philippe; Rossi, Andrea; Roukoutakis, Filimon; Roy, Ankhi; Roy, Christelle Sophie; Roy, Pradip Kumar; Rubio Montero, Antonio Juan; Rui, Rinaldo; Russo, Riccardo; Ryabinkin, Evgeny; Ryabov, Yury; Rybicki, Andrzej; Sadovskiy, Sergey; Safarik, Karel; Sahlmuller, Baldo; Sahoo, Pragati; Sahoo, Raghunath; Sahoo, Sarita; Sahu, Pradip Kumar; Saini, Jogender; Sakai, Shingo; Saleh, Mohammad Ahmad; Salgado Lopez, Carlos Alberto; Salzwedel, Jai Samuel Nielsen; Sambyal, Sanjeev Singh; Samsonov, Vladimir; Sanchez Castro, Xitzel; Sandor, Ladislav; Sandoval, Andres; Sano, Masato; Santagati, Gianluca; Sarkar, Debojit; Scapparone, Eugenio; Scarlassara, Fernando; Scharenberg, Rolf Paul; Schiaua, Claudiu Cornel; Schicker, Rainer Martin; Schmidt, Christian Joachim; Schmidt, Hans Rudolf; Schuchmann, Simone; Schukraft, Jurgen; Schulc, Martin; Schuster, Tim Robin; Schutz, Yves Roland; Schwarz, Kilian Eberhard; Schweda, Kai Oliver; Scioli, Gilda; Scomparin, Enrico; Scott, Rebecca Michelle; Seeder, Karin Soraya; Seger, Janet Elizabeth; Sekiguchi, Yuko; Selyuzhenkov, Ilya; Senosi, Kgotlaesele; Seo, Jeewon; Serradilla Rodriguez, Eulogio; Sevcenco, Adrian; Shabanov, Arseniy; Shabetai, Alexandre; Shadura, Oksana; Shahoyan, Ruben; Shangaraev, Artem; Sharma, Ankita; Sharma, Natasha; Shigaki, Kenta; Shtejer Diaz, Katherin; Sibiryak, Yury; Siddhanta, Sabyasachi; Sielewicz, Krzysztof Marek; Siemiarczuk, Teodor; Silvermyr, David Olle Rickard; Silvestre, Catherine Micaela; Simatovic, Goran; Simonetti, Giuseppe; Singaraju, Rama Narayana; Singh, Ranbir; Singha, Subhash; Singhal, Vikas; Sinha, Bikash; Sarkar - Sinha, Tinku; Sitar, Branislav; Sitta, Mario; Skaali, Bernhard; Slupecki, Maciej; Smirnov, Nikolai; Snellings, Raimond; Snellman, Tomas Wilhelm; Soegaard, Carsten; Soltz, Ron Ariel; Song, Jihye; Song, Myunggeun; Song, Zixuan; Soramel, Francesca; Sorensen, Soren Pontoppidan; Spacek, Michal; Spiriti, Eleuterio; Sputowska, Iwona Anna; Spyropoulou-Stassinaki, Martha; Srivastava, Brijesh Kumar; Stachel, Johanna; Stan, Ionel; Stefanek, Grzegorz; Steinpreis, Matthew Donald; Stenlund, Evert Anders; Steyn, Gideon Francois; Stiller, Johannes Hendrik; Stocco, Diego; Strmen, Peter; Alarcon Do Passo Suaide, Alexandre; Sugitate, Toru; Suire, Christophe Pierre; Suleymanov, Mais Kazim Oglu; Sultanov, Rishat; Sumbera, Michal; Symons, Timothy; Szabo, Alexander; Szanto De Toledo, Alejandro; Szarka, Imrich; Szczepankiewicz, Adam; Szymanski, Maciej Pawel; Takahashi, Jun; Tanaka, Naoto; Tangaro, Marco-Antonio; Tapia Takaki, Daniel Jesus; Tarantola Peloni, Attilio; Tariq, Mohammad; Tarzila, Madalina-Gabriela; Tauro, Arturo; Tejeda Munoz, Guillermo; Telesca, Adriana; Terasaki, Kohei; Terrevoli, Cristina; Teyssier, Boris; Thaeder, Jochen Mathias; Thomas, Deepa; Tieulent, Raphael Noel; Timmins, Anthony Robert; Toia, Alberica; Trogolo, Stefano; Trubnikov, Victor; Trzaska, Wladyslaw Henryk; Tsuji, Tomoya; Tumkin, Alexandr; Turrisi, Rosario; Tveter, Trine Spedstad; Ullaland, Kjetil; Uras, Antonio; Usai, Gianluca; Utrobicic, Antonija; Vajzer, Michal; Vala, Martin; Valencia Palomo, Lizardo; Vallero, Sara; Van Der Maarel, Jasper; Van Hoorne, Jacobus Willem; Van Leeuwen, Marco; Vanat, Tomas; Vande Vyvre, Pierre; Varga, Dezso; Diozcora Vargas Trevino, Aurora; Vargyas, Marton; Varma, Raghava; Vasileiou, Maria; Vasiliev, Andrey; Vauthier, Astrid; Vechernin, Vladimir; Veen, Annelies Marianne; Veldhoen, Misha; Velure, Arild; Venaruzzo, Massimo; Vercellin, Ermanno; Vergara Limon, Sergio; Vernet, Renaud; Verweij, Marta; Vickovic, Linda; Viesti, Giuseppe; Viinikainen, Jussi Samuli; Vilakazi, Zabulon; Villalobos Baillie, Orlando; Vinogradov, Alexander; Vinogradov, Leonid; Vinogradov, Yury; Virgili, Tiziano; Vislavicius, Vytautas; Viyogi, Yogendra; Vodopyanov, Alexander; Volkl, Martin Andreas; Voloshin, Kirill; Voloshin, Sergey; Volpe, Giacomo; Von Haller, Barthelemy; Vorobyev, Ivan; Vranic, Danilo; Vrlakova, Janka; Vulpescu, Bogdan; Vyushin, Alexey; Wagner, Boris; Wagner, Jan; Wang, Hongkai; Wang, Mengliang; Wang, Yifei; Watanabe, Daisuke; Weber, Michael; Weber, Steffen Georg; Wessels, Johannes Peter; Westerhoff, Uwe; Wiechula, Jens; Wikne, Jon; Wilde, Martin Rudolf; Wilk, Grzegorz Andrzej; Wilkinson, Jeremy John; Williams, Crispin; Windelband, Bernd Stefan; Winn, Michael Andreas; Yaldo, Chris G; Yamaguchi, Yorito; Yang, Hongyan; Yang, Ping; Yano, Satoshi; Yasnopolskiy, Stanislav; Yin, Zhongbao; Yokoyama, Hiroki; Yoo, In-Kwon; Yurchenko, Volodymyr; Yushmanov, Igor; Zaborowska, Anna; Zaccolo, Valentina; Zaman, Ali; Zampolli, Chiara; Correia Zanoli, Henrique Jose; Zaporozhets, Sergey; Zarochentsev, Andrey; Zavada, Petr; Zavyalov, Nikolay; Zbroszczyk, Hanna Paulina; Zgura, Sorin Ion; Zhalov, Mikhail; Zhang, Haitao; Zhang, Xiaoming; Zhang, Yonghong; Zhao, Chengxin; Zhigareva, Natalia; Zhou, Daicui; Zhou, You; Zhou, Zhuo; Zhu, Hongsheng; Zhu, Jianhui; Zhu, Xiangrong; Zichichi, Antonino; Zimmermann, Alice; Zimmermann, Markus Bernhard; Zinovjev, Gennady; Zyzak, Maksym

    2016-01-10

    We present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possible $\\overline{\\Lambda\\mathrm{n}}$ bound state. The search is performed with the ALICE detector in central (0-10%) Pb-Pb collisions at $ \\sqrt{s_{\\rm{NN}}} = 2.76$ TeV, by invariant mass analysis in the decay modes $\\overline{\\Lambda\\mathrm{n}} \\rightarrow \\overline{\\mathrm{d}} \\pi^{+} $ and H-dibaryon $\\rightarrow \\Lambda \\mathrm{p} \\pi^{-}$. No evidence for these bound states is observed. Upper limits are determined at 99% confidence level for a wide range of lifetimes and for the full range of branching ratios. The results are compared to thermal, coalescence and hybrid UrQMD model expectations, which describe correctly the production of other loosely bound states, like the deuteron and the hypertriton.

  17. Search for weakly decaying Λn‾ and ΛΛ exotic bound states in central Pb–Pb collisions at sNN=2.76 TeV

    Directory of Open Access Journals (Sweden)

    J. Adam

    2016-01-01

    Full Text Available We present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possible Λn‾ bound state. The search is performed with the ALICE detector in central (0–10% Pb–Pb collisions at sNN=2.76 TeV, by invariant mass analysis in the decay modes Λn‾→d‾π+ and H-dibaryon →Λpπ−. No evidence for these bound states is observed. Upper limits are determined at 99% confidence level for a wide range of lifetimes and for the full range of branching ratios. The results are compared to thermal, coalescence and hybrid UrQMD model expectations, which describe correctly the production of other loosely bound states, like the deuteron and the hypertriton.

  18. Structural Characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole

    Science.gov (United States)

    Chen, Chiung-Kuang; Leung, Siegfried S. F.; Guilbert, Christophe; Jacobson, Matthew P.; McKerrow, James H.; Podust, Larissa M.

    2010-01-01

    Background Chagas Disease is the leading cause of heart failure in Latin America. Current drug therapy is limited by issues of both efficacy and severe side effects. Trypansoma cruzi, the protozoan agent of Chagas Disease, is closely related to two other major global pathogens, Leishmania spp., responsible for leishmaniasis, and Trypansoma brucei, the causative agent of African Sleeping Sickness. Both T. cruzi and Leishmania parasites have an essential requirement for ergosterol, and are thus vulnerable to inhibitors of sterol 14α-demethylase (CYP51), which catalyzes the conversion of lanosterol to ergosterol. Clinically employed anti-fungal azoles inhibit ergosterol biosynthesis in fungi, and specific azoles are also effective against both Trypanosoma and Leishmania parasites. However, modification of azoles to enhance efficacy and circumvent potential drug resistance has been problematic for both parasitic and fungal infections due to the lack of structural insights into drug binding. Methodology/Principal Findings We have determined the crystal structures for CYP51 from T. cruzi (resolutions of 2.35 Å and 2.27 Å), and from the related pathogen T. brucei (resolutions of 2.7 Å and 2.6 Å), co-crystallized with the antifungal drugs fluconazole and posaconazole. Remarkably, both drugs adopt multiple conformations when binding the target. The fluconazole 2,4-difluorophenyl ring flips 180° depending on the H-bonding interactions with the BC-loop. The terminus of the long functional tail group of posaconazole is bound loosely in the mouth of the hydrophobic substrate binding tunnel, suggesting that the major contribution of the tail to drug efficacy is for pharmacokinetics rather than in interactions with the target. Conclusions/Significance The structures provide new insights into binding of azoles to CYP51 and mechanisms of potential drug resistance. Our studies define in structural detail the CYP51 therapeutic target in T. cruzi, and offer a starting point for

  19. Pore-scale structure of a NAPL front during invasion into strongly and weakly water-wetting sands

    Science.gov (United States)

    Molnar, I. L.; Willson, C. S.; O'Carroll, D. M.; Gerhard, J.

    2016-12-01

    An improved understanding of the mechanisms governing Non-Aqueous Phase Liquid (NAPL) transport through porous media is critical to solving a number of important environmental problems (e.g., transport and remediation of chlorinated solvents to carbon sequestration in deep brine aquifers for long-term storage). The pore-scale distribution of NAPL governs the efficiency of remedial activities and trapping processes. Understanding the pore-scale distribution of NAPL during water drainage and imbibition is vital to improving continuum-scale models. While these models may reasonably predict NAPL saturation, they may rely on potentially incorrect assumptions of pore-scale NAPL distribution to assess relative permeability or dissolution rates. Until recently, most pore-scale studies have focused on residual NAPL following water imbibition with little emphasis on examining pore-scale behaviour during water drainage. As a result, the pore-scale structure of the drainage front remains poorly understood. In addition, almost no studies have examined how wettability, a major factor impacting pore-scale NAPL distribution, influences the pore-scale structure of the drainage front. This study examines the pore-scale distribution of a tetrachloroethylene/surfactant mixture during water drainage in strongly (iron oxide) and weakly water-wetting (quartz) sands. Dodecylamine was used to render quartz media weakly water wetting while keeping iron oxide strongly water wetting. SXCMT was employed to image the length of the front during drainage. Absorption-edge imaging was employed to segment the grain, water and NAPL phases followed by extensive characterization of the segmented pore network and fluid distributions. Comparing and contrasting the high resolution quartz and iron oxide datasets highlights the wettability mechanisms responsible for changes in continuum-scale flow and dissolution relationships. Specific attention was placed on examining capillary pressure as a function of

  20. Measuring dynamics in weakly structured regions of proteins using microfluidics-enabled subsecond H/D exchange mass spectrometry.

    Science.gov (United States)

    Rob, Tamanna; Liuni, Peter; Gill, Preet Kamal; Zhu, Shaolong; Balachandran, Naresh; Berti, Paul J; Wilson, Derek J

    2012-04-17

    This work introduces an integrated microfluidic device for measuring rapid H/D exchange (HDX) in proteins. By monitoring backbone amide HDX on the millisecond to low second time scale, we are able to characterize conformational dynamics in weakly structured regions, such as loops and molten globule-like domains that are inaccessible in conventional HDX experiments. The device accommodates the entire MS-based HDX workflow on a single chip with residence times sufficiently small (ca. 8 s) that back-exchange is negligible (≤5%), even without cooling. Components include an adjustable position capillary mixer providing a variable-time labeling pulse, a static mixer for HDX quenching, a proteolytic microreactor for rapid protein digestion, and on-chip electrospray ionization (ESI). In the present work, we characterize device performance using three model systems, each illustrating a different application of 'time-resolved' HDX. Ubiquitin is used to illustrate a crude, high throughput structural analysis based on a single subsecond HDX time-point. In experiments using cytochrome c, we distinguish dynamic behavior in loops, establishing a link between flexibility and interactions with the heme prosthetic group. Finally, we localize an unusually high 'burst-phase' of HDX in the large tetrameric enzyme DAHP synthase to a 'molten globule-like' region surrounding the active site.

  1. Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics.

    Science.gov (United States)

    Wise-Scira, Olivia; Xu, Liang; Perry, George; Coskuner, Orkid

    2012-08-01

    Binding of divalent metal ions with intrinsically disordered fibrillogenic proteins, such as amyloid-β (Aβ), influences the aggregation process and the severity of neurodegenerative diseases. The Aβ monomers and oligomers are the building blocks of the aggregates. In this work, we report the structures and free energy landscapes of the monomeric zinc(II)-bound Aβ40 (Zn:Aβ40) and zinc(II)-bound Aβ42 (Zn:Aβ42) intrinsically disordered fibrillogenic metallopeptides in an aqueous solution by utilizing an approach that employs first principles calculations and parallel tempering molecular dynamics simulations. The structural and thermodynamic properties, including the secondary and tertiary structures and conformational Gibbs free energies of these intrinsically disordered metallopeptide alloforms, are presented. The results show distinct differing characteristics for these metallopeptides. For example, prominent β-sheet formation in the N-terminal region (Asp1, Arg5, and Tyr10) of Zn:Aβ40 is significantly decreased or lacking in Zn:Aβ42. Our findings indicate that blocking multiple reactive residues forming abundant β-sheet structure located in the central hydrophobic core and C-terminal regions of Zn:Aβ42 via antibodies or small organic molecules might help to reduce the aggregation of Zn(II)-bound Aβ42. Furthermore, we find that helix formation increases but β-sheet formation decreases in the C-terminal region upon Zn(II) binding to Aβ. This depressed β-sheet formation in the C-terminal region (Gly33-Gly38) in monomeric Zn:Aβ42 might be linked to the formation of amorphous instead of fibrillar aggregates of Zn:Aβ42.

  2. Switched or not?: the structure of unphosphorylated CheY bound to the N terminus of FliM.

    Science.gov (United States)

    Dyer, Collin M; Dahlquist, Frederick W

    2006-11-01

    Phosphorylation of Escherichia coli CheY increases its affinity for its target, FliM, 20-fold. The interaction between BeF(3)(-)-CheY, a phosphorylated CheY (CheY approximately P) analog, and the FliM sequence that it binds has been described previously in molecular detail. Although the conformation that unphosphorylated CheY adopts in complex with FliM was unknown, some evidence suggested that it is similar to that of CheY approximately P. To resolve the issue, we have solved the crystallographic structure of unphosphorylated, magnesium(II)-bound CheY in complex with a synthetic peptide corresponding to the target region of FliM (the 16 N-terminal residues of FliM [FliM(16)]). While the peptide conformation and binding site are similar to those of the BeF(3)(-)-CheY-FliM(16) complex, the inactive CheY conformation is largely retained in the unphosphorylated Mg(2+)-CheY-FliM(16) complex. Communication between the target binding site and the phosphorylation site, observed previously in biochemical experiments, is enabled by a network of conserved side chain interactions that partially mimic those observed in BeF(3)(-)-activated CheY. This structure makes clear the active role that the beta4-alpha4 loop plays in the Tyr(87)-Tyr(106) coupling mechanism that enables allosteric communication between the phosphorylation site and the target binding surface. Additionally, this structure provides a high-resolution view of an intermediate conformation of a response regulator protein, which had been generally assumed to be two state.

  3. Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae

    Science.gov (United States)

    Unno, Masaki; Ardèvol, Albert; Rovira, Carme; Ikeda-Saito, Masao

    2013-01-01

    Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe3+-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe3+-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe3+-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe3+-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit. PMID:24106279

  4. Stimulation of Tetrabromobisphenol A Binding to Soil Humic Substances by Birnessite and the Chemical Structure of the Bound Residues.

    Science.gov (United States)

    Tong, Fei; Gu, Xueyuan; Gu, Cheng; Xie, Jinyu; Xie, Xianchuan; Jiang, Bingqi; Wang, Yongfeng; Ertunc, Tanya; Schäffer, Andreas; Ji, Rong

    2016-06-21

    Studies have shown the main fate of the flame retardant tetrabromobisphenol A (TBBPA) in soils is the formation of bound residues, and mechanisms on it are less-understood. This study investigated the effect of birnessite (δ-MnO2), a naturally occurring oxidant in soils, on the formation of bound residues. (14)C-labeled TBBPA was used to investigate the pH dependency of TBBPA bound-residue formation to two soil humic acids (HAs), Elliott soil HA and Steinkreuz soil HA, in the presence of δ-MnO2. The binding of TBBPA and its transformation products to both HAs was markedly increased (3- to 17-fold) at all pH values in the presence of δ-MnO2. More bound residues were formed with the more aromatic Elliott soil HA than with Steinkreuz soil HA. Gel-permeation chromatography revealed a uniform distribution of the bound residues within Steinkreuz soil HA and a nonuniform distribution within Elliott soil HA. (13)C NMR spectroscopy of (13)C-TBBPA residues bound to (13)C-depleted HA suggested that in the presence of δ-MnO2, binding occurred via ester and ether and other types of covalent bonds besides HA sequestration. The insights gained in this study contribute to an understanding of the formation of TBBPA bound residues facilitated by δ-MnO2.

  5. Quantum transport through a quantum dot structure side coupled with many quantum-dot and Majorana-bound-state pairs

    Directory of Open Access Journals (Sweden)

    Z. T. Jiang

    2016-12-01

    Full Text Available We theoretically investigate the electron transport properties of a wheel-like quantum dot (QD structure with a central QD side coupled with many pairs of QD and Majorana bound states (MBSs by using the nonequilibrium Green’s function method. For clarity, we concentrate our researches on the parameter regime where interdot couplings is much smaller than the inter-MBS and MBS-QD couplings, which ensures the conductance peaks induced by them distinguishable. In the absence of the interdot couplings among the side QDs, the increase of the MBS-QD pair number is equivalent to the increase of the interdot coupling in the QD structure including one central QD and one MBS-QD pair. It is shown that as a response the interval between two side symmetrical peaks will be enlarged, and the MBS-QD couplings will bring into being a zero-bias conductance peak which can be split into two symmetrical sub-peaks by the nonzero inter-MBS couplings. In the presence of the interdot couplings among the side QDs, they make serious influences on the conductance peaks determined by the QD energy levels, and still comes into being the zero-bias conductance peak due to the MBS-QD couplings, yet which is split into two asymmetrical sub-peaks under the influences of the nonzero inter-MBS couplings. Moreover, we conduct a detailed investigation into how the couplings among side QDs affect the transport properties, clearly exposing the underneath mechanics responsible for producing these phenomena. Finally, a generalization is made so as to discuss the geometry universality and the parameter universality of the conclusion drawn in the present work. It should be emphasized that this research will be helpful for a comprehensive understanding the quantum transport through the QD systems coupled with MBSs.

  6. Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.

    Science.gov (United States)

    Zeng, Fuxing; Chen, Yanbo; Remis, Jonathan; Shekhar, Mrinal; Phillips, James C; Tajkhorshid, Emad; Jin, Hong

    2017-01-26

    Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.

  7. Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site.

    Science.gov (United States)

    Ramelot, Theresa A; Cort, John R; Goldsmith-Fischman, Sharon; Kornhaber, Gregory J; Xiao, Rong; Shastry, Ritu; Acton, Thomas B; Honig, Barry; Montelione, Gaetano T; Kennedy, Michael A

    2004-11-19

    IscU is a highly conserved protein that serves as the scaffold for IscS-mediated assembly of iron-sulfur ([Fe-S]) clusters. We report the NMR solution structure of monomeric Haemophilus influenzae IscU with zinc bound at the [Fe-S] cluster assembly site. The compact core of the globular structure has an alpha-beta sandwich architecture with a three-stranded antiparallel beta-sheet and four alpha-helices. A nascent helix is located N-terminal to the core structure. The zinc is ligated by three cysteine residues and one histidine residue that are located in and near conformationally dynamic loops at one end of the IscU structure. Removal of the zinc metal by chelation results in widespread loss of structure in the apo form. The zinc-bound IscU may be a good model for iron-loaded IscU and may demonstrate structural features found in the [Fe-S] cluster bound form. Structural and functional similarities, genomic context in operons containing other homologous genes, and distributions of conserved surface residues support the hypothesis that IscU protein domains are homologous (i.e. derived from a common ancestor) with the SufE/YgdK family of [Fe-S] cluster assembly proteins.

  8. Space group constraints on weak indices in topological insulators

    Science.gov (United States)

    Varjas, Dániel; de Juan, Fernando; Lu, Yuan-Ming

    2017-07-01

    Lattice translation symmetry gives rise to a large class of "weak" topological insulators (TIs), characterized by translation-protected gapless surface states and dislocation bound states. In this work we show that space group symmetries lead to constraints on the weak topological indices that define these phases. In particular, we show that screw rotation symmetry enforces the Hall conductivity in planes perpendicular to the screw axis to be quantized in multiples of the screw rank, which generally applies to interacting systems. We further show that certain 3D weak indices associated with quantum spin Hall effects (class AII) are forbidden by the Bravais lattice and by glide or even-fold screw symmetries. These results put strong constraints on weak TI candidates in the experimental and numerical search for topological materials, based on the crystal structure alone.

  9. Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design

    Energy Technology Data Exchange (ETDEWEB)

    Sprenger, Janina [Lund University, SE-221 00 Lund (Sweden); Lund University, SE-221 84 Lund (Sweden); Svensson, Bo [Lund University, SE-221 00 Lund (Sweden); SARomics Biostructures AB, Box 724, SE-220 07 Lund (Sweden); Hålander, Jenny [Lund University, SE-221 00 Lund (Sweden); Carey, Jannette [Princeton University, Princeton, New Jersey (United States); Persson, Lo [Lund University, SE-221 84 Lund (Sweden); Al-Karadaghi, Salam, E-mail: salam.al-karadaghi@biochemistry.lu.se [Lund University, SE-221 00 Lund (Sweden)

    2015-03-01

    In this work, X-ray crystallography was used to examine ligand complexes of spermidine synthase from the malaria parasite Plasmodium falciparum (PfSpdS). The enzymes of the polyamine-biosynthesis pathway have been proposed to be promising drug targets in the treatment of malaria. Spermidine synthase (SpdS; putrescine aminopropyltransferase) catalyzes the transfer of the aminopropyl moiety from decarboxylated S-adenosylmethionine to putrescine, leading to the formation of spermidine and 5′-methylthioadenosine (MTA). In this work, X-ray crystallography was used to examine ligand complexes of SpdS from the malaria parasite Plasmodium falciparum (PfSpdS). Five crystal structures were determined of PfSpdS in complex with MTA and the substrate putrescine, with MTA and spermidine, which was obtained as a result of the enzymatic reaction taking place within the crystals, with dcAdoMet and the inhibitor 4-methylaniline, with MTA and 4-aminomethylaniline, and with a compound predicted in earlier in silico screening to bind to the active site of the enzyme, benzimidazol-(2-yl)pentan-1-amine (BIPA). In contrast to the other inhibitors tested, the complex with BIPA was obtained without any ligand bound to the dcAdoMet-binding site of the enzyme. The complexes with the aniline compounds and BIPA revealed a new mode of ligand binding to PfSpdS. The observed binding mode of the ligands, and the interplay between the two substrate-binding sites and the flexible gatekeeper loop, can be used in the design of new approaches in the search for new inhibitors of SpdS.

  10. Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition.

    Science.gov (United States)

    Gautam, Gunjan; Rehman, Syed Arif Abdul; Pandey, Preeti; Gourinath, Samudrala

    2017-08-01

    The versatility in the recognition of various interacting proteins by the SH3 domain drives a variety of cellular functions. Here, the crystal structure of the C-terminal SH3 domain of myosin IB from Entamoeba histolytica (EhMySH3) is reported at a resolution of 1.7 Å in native and PEG-bound states. Comparisons with other structures indicated that the PEG molecules occupy protein-protein interaction pockets similar to those occupied by the peptides in other peptide-bound SH3-domain structures. Also, analysis of the PEG-bound EhMySH3 structure led to the recognition of two additional pockets, apart from the conventional polyproline and specificity pockets, that are important for ligand interaction. Molecular-docking studies combined with various comparisons revealed structural similarity between EhMySH3 and the SH3 domain of β-Pix, and this similarity led to the prediction that EhMySH3 preferentially binds targets containing type II-like PXXP motifs. These studies expand the understanding of the EhMySH3 domain and provide extensive structural knowledge, which is expected to help in predicting the interacting partners which function together with myosin IB during phagocytosis in E. histolytica infections.

  11. Weak relativity

    CERN Document Server

    Selleri, Franco

    2015-01-01

    Weak Relativity is an equivalent theory to Special Relativity according to Reichenbach’s definition, where the parameter epsilon equals to 0. It formulates a Neo-Lorentzian approach by replacing the Lorentz transformations with a new set named “Inertial Transformations”, thus explaining the Sagnac effect, the twin paradox and the trip from the future to the past in an easy and elegant way. The cosmic microwave background is suggested as a possible privileged reference system. Most importantly, being a theory based on experimental proofs, rather than mutual consensus, it offers a physical description of reality independent of the human observation.

  12. Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A.; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K. (Stanford-MED); (ConfometRx); (UCB Pharma)

    2017-02-06

    The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl D-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.

  13. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    nuclear physics changed drastically as the new generation of accelerators started providing more and more rare isotopes, which are away from the line of stability. These weakly bound nuclei are found to exhibit new forms of nuclear matter and unprecedented exotic behaviour. The low breakup thresholds of these rare ...

  14. Homogenization-based interval analysis for structural-acoustic problem involving periodical composites and multi-scale uncertain-but-bounded parameters.

    Science.gov (United States)

    Chen, Ning; Yu, Dejie; Xia, Baizhan; Liu, Jian; Ma, Zhengdong

    2017-04-01

    This paper presents a homogenization-based interval analysis method for the prediction of coupled structural-acoustic systems involving periodical composites and multi-scale uncertain-but-bounded parameters. In the structural-acoustic system, the macro plate structure is assumed to be composed of a periodically uniform microstructure. The equivalent macro material properties of the microstructure are computed using the homogenization method. By integrating the first-order Taylor expansion interval analysis method with the homogenization-based finite element method, a homogenization-based interval finite element method (HIFEM) is developed to solve a periodical composite structural-acoustic system with multi-scale uncertain-but-bounded parameters. The corresponding formulations of the HIFEM are deduced. A subinterval technique is also introduced into the HIFEM for higher accuracy. Numerical examples of a hexahedral box and an automobile passenger compartment are given to demonstrate the efficiency of the presented method for a periodical composite structural-acoustic system with multi-scale uncertain-but-bounded parameters.

  15. Apo And Calcium-Bound Crystal Structures of Alpha-11 Giardin, An Unusual Annexin From 'Giardia Lamblia'

    Energy Technology Data Exchange (ETDEWEB)

    Pathuri, P.; Nguyen, E.T.; Svard, S.G.; Luecke, H.; /UC, Irvine /Uppsala U. /Karolinska Inst.

    2007-07-12

    Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids. Several alpha giardins are highly expressed during parasite-induced diarrhea in humans. Despite being a member of a large family of proteins, little is known about the function and cellular localization of alpha-11 giardin, although giardins are often associated with the cytoskeleton. It has been shown that Giardia exhibits high levels of alpha-11 giardin mRNA transcript throughout its life cycle; however, constitutive over-expression of this protein is lethal to the parasite. Determining the three-dimensional structure of an alpha-giardin is essential to identifying functional domains shared in the alpha-giardin family. Here we report the crystal structures of the apo and Ca{sup 2+}-bound forms of alpha-11 giardin, the first alpha giardin to be characterized structurally. Crystals of apo and Ca{sup 2+}-bound alpha-11 giardin diffracted to 1.1 angstroms and 2.93 angstroms, respectively. The crystal structure of selenium-substituted apo alpha-11 giardin reveals a planar array of four tandem repeats of predominantly {alpha}-helical domains, reminiscent of previously determined annexin structures, making this the highest-resolution structure of an annexin to date. The apo alpha-11 giardin structure also reveals a hydrophobic core formed between repeats I/IV and II/III, a region typically hydrophilic in other annexins. Surprisingly, the Ca{sup 2+}-bound structure contains only a single calcium ion, located in the DE loop of repeat I and coordinated differently from the two types of calcium sites observed in previous annexin structures. The apo and Ca{sup 2+}-bound alpha-11 giardin structures assume overall similar conformations; however, Ca2+-bound alpha-11 giardin crystallized in a lower

  16. Regularity of Tor for weakly stable ideals

    Directory of Open Access Journals (Sweden)

    Katie Ansaldi

    2015-05-01

    Full Text Available It is proved that if I and J are weakly stable ideals in a polynomial ring R = k[x_1, . . ., x_n], with k a field, then the regularity of Tor^R_i (R/I, R/J has the expected upper bound. We also give a bound for the regularity of Ext^i_R (R/I, R for I a weakly stable ideal.

  17. Bound Exciton Complexes

    Science.gov (United States)

    Meyer, B. K.

    In the preceding chapter, we concentrated on the properties of free excitons. These free excitons may move through the sample and hit a trap, a nonradiative or a radiative recombination center. At low temperatures, the latter case gives rise to either deep center luminescence, mentioned in Sect. 7.1 and discussed in detail in Chap. 9, or to the luminescence of bound exciton complexes (BE or BEC). The chapter continues with the most prominent of these BECs, namely A-excitons bound to neutral donors. The next aspects are the more weakly BEs at ionized donors. The Sect. 7.4 treats the binding or localization energies of BEC from a theoretical point of view, while Sect. 7.5 is dedicated to excited states of BECs, which contain either holes from deeper valence bands or an envelope function with higher quantum numbers. The last section is devoted to donor-acceptor pair transitions. There is no section devoted specifically to excitons bound to neutral acceptors, because this topic is still partly controversially discussed. Instead, information on these A0X complexes is scattered over the whole chapter, however, with some special emphasis seen in Sects. 7.1, 7.4, and 7.5.

  18. Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Rong; Munger, Christine; Asinas, Abdalin; Benoit, Stephane L.; Miller, Erica; Matte, Allan; Maier, Robert J.; Cygler, Miroslaw (McGill); (Georgia); (Biotech Res.)

    2010-10-22

    The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 {angstrom} resolution, bound to Cu{sup 2+} at 2.7 {angstrom} resolution, and bound to Ni{sup 2+} at 3.1 {angstrom} resolution. Apo UreE forms dimers, while the metal-bound enzymes are arranged as tetramers that consist of a dimer of dimers associated around the metal ion through coordination by His102 residues from each subunit of the tetramer. Comparison of independent subunits from different crystal forms indicates changes in the relative arrangement of the N- and C-terminal domains in response to metal binding. The improved ability of engineered versions of UreE containing hexahistidine sequences at either the N-terminal or C-terminal end to provide Ni{sup 2+} for the final metal sink (urease) is eliminated in the H102A version. Therefore, the ability of the improved Ni{sup 2+}-binding versions to deliver more nickel is likely an effect of an increased local concentration of metal ions that can rapidly replenish transferred ions bound to His102.

  19. Rigorous coherent-structure theory for falling liquid films: Viscous dispersion effects on bound-state formation and self-organization

    Science.gov (United States)

    Pradas, Marc; Tseluiko, Dmitri; Kalliadasis, Serafim

    2011-04-01

    We examine the interaction of two-dimensional solitary pulses on falling liquid films. We make use of the second-order model derived by Ruyer-Quil and Manneville [Eur. Phys. J. B 6, 277 (1998); Eur. Phys. J. B 15, 357 (2000); Phys. Fluids 14, 170 (2002)] by combining the long-wave approximation with a weighted residual technique. The model includes (second-order) viscous dispersion effects which originate from the streamwise momentum equation and tangential stress balance. These effects play a dispersive role that primarily influences the shape of the capillary ripples in front of the solitary pulses. We show that different physical parameters, such as surface tension and viscosity, play a crucial role in the interaction between solitary pulses giving rise eventually to the formation of bound states consisting of two or more pulses separated by well-defined distances and traveling at the same velocity. By developing a rigorous coherent-structure theory, we are able to theoretically predict the pulse-separation distances for which bound states are formed. Viscous dispersion affects the distances at which bound states are observed. We show that the theory is in very good agreement with computations of the second-order model. We also demonstrate that the presence of bound states allows the film free surface to reach a self-organized state that can be statistically described in terms of a gas of solitary waves separated by a typical mean distance and characterized by a typical density.

  20. Muscle Weakness

    Directory of Open Access Journals (Sweden)

    Ali Al Kaissi MD, MSc

    2017-01-01

    Full Text Available Marked ligamentous hyperlaxity and muscle weakness/wasting associated with awkward gait are the main deficits confused with the diagnosis of myopathy. Seven children (6 boys and 1 girl with an average age of 8 years were referred to our department because of diverse forms of skeletal abnormalities. No definitive diagnosis was made, and all underwent a series of sophisticated investigations in other institutes in favor of myopathy. We applied our methodology through the clinical and radiographic phenotypes followed by targeted genotypic confirmation. Three children (2 boys and 1 girl were compatible with the diagnosis of progressive pseudorheumatoid chondrodysplasia. The genetic mutation was correlated with the WISP 3 gene actively expressed by articular chondrocytes and located on chromosome 6. Klinefelter syndrome was the diagnosis in 2 boys. Karyotyping confirmed 47,XXY (aneuploidy of Klinefelter syndrome. And 2 boys were finally diagnosed with Morquio syndrome (MPS type IV A as both showed missense mutations in the N-acetylgalactosamine-sulfate sulfatase gene. Misdiagnosis can lead to the initiation of a long list of sophisticated investigations.

  1. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio

    2012-03-01

    Full Text Available The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models. The goal of this paper is to illustrate the difficulties involved in providing a correct definition of what a rational (or irrational agent is. In this paper we describe two frameworks that employ different approaches for analyzing bounded rationality. The first is a spatial segregation set-up that encompasses two optimization methodologies: backward induction and forward induction. The main result is that, even under the same state of knowledge, rational and non-rational agents may match their actions. The second framework elaborates on the relationship between irrationality and informational restrictions. We use the beauty contest (Nagel, 1995 as a device to explain this relationship.

    La observación del comportamiento de los agentes económicos tanto en el laboratorio como en la vida real justifica que la racionalidad acotada sea un supuesto aceptado en numerosos modelos socio-económicos. El objetivo de este artículo es ilustrar las dificultades que conlleva una correcta definición de qué es un agente racional (irracional. En este artículo se describen dos marcos que emplean diferentes metodologías para analizar la racionalidad acotada. El primero es un modelo de segregación espacial donde se contrastan dos metodologías de optimización: inducción hacia atrás y hacia adelante. El resultado principal es que, incluso con el mismo nivel de conocimiento, tanto agentes racionales como irracionales podrían coincidir en sus acciones. El segundo marco trabaja sobre la relación entre irracionalidad y restricción de información. Se utiliza el juego llamado “beauty contest” (Nagel 1995 como mecanismo para explicar dicha relación.

  2. Weak bond screening system

    Science.gov (United States)

    Chuang, S. Y.; Chang, F. H.; Bell, J. R.

    Consideration is given to the development of a weak bond screening system which is based on the utilization of a high power ultrasonic (HPU) technique. The instrumentation of the prototype bond strength screening system is described, and the adhesively bonded specimens used in the system developmental effort are detailed. Test results obtained from these specimens are presented in terms of bond strength and level of high power ultrasound irradiation. The following observations were made: (1) for Al/Al specimens, 2.6 sec of HPU irradiation will screen weak bond conditions due to improper preparation of bonding surfaces; (2) for composite/composite specimens, 2.0 sec of HPU irradiation will disrupt weak bonds due to under-cured conditions; (3) for Al honeycomb core with composite skin structure, 3.5 sec of HPU irradiation will disrupt weak bonds due to bad adhesive or oils contamination of bonding surfaces; and (4) for Nomex honeycomb with Al skin structure, 1.3 sec of HPU irradiation will disrupt weak bonds due to bad adhesive.

  3. Charged weak currents

    CERN Document Server

    Turlay, René

    1979-01-01

    In this review of charged weak currents the author concentrates on inclusive high energy neutrino physics. The authors discusses the general structure of charged currents, new results on total cross- sections, the Callan-Gross relation, antiquark distributions, scaling violations and tests of QCD. A very short summary on multilepton physics is given. (44 refs).

  4. Crystal Structure of the Redox-Active Cofactor Dibromothymoquinone Bound to Circadian Clock Protein KaiA and Structural Basis for Dibromothymoquinone's Ability to Prevent Stimulation of KaiC Phosphorylation by KaiA

    Energy Technology Data Exchange (ETDEWEB)

    Pattanayek, Rekha; Sidiqi, Said K.; Egli, Martin [Vanderbilt-MED

    2013-09-19

    KaiA protein that stimulates KaiC phosphorylation in the cyanobacterial circadian clock was recently shown to be destabilized by dibromothymoquinone (DBMIB), thus revealing KaiA as a sensor of the plastoquinone (PQ) redox state and suggesting an indirect control of the clock by light through PQ redox changes. Here we show using X-ray crystallography that several DBMIBs are bound to KaiA dimer. Some binding modes are consistent with oligomerization of N-terminal KaiA pseudoreceiver domains and/or reduced interdomain flexibility. DBMIB bound to the C-terminal KaiA (C-KaiA) domain and limited stimulation of KaiC kinase activity by C-KaiA in the presence of DBMIB demonstrate that the cofactor may weakly inhibit KaiA-KaiC binding.

  5. Structural Evidence for a Copper-Bound Carbonate Intermediate in the Peroxidase and Dismutase Activities of Superoxide Dismutase

    OpenAIRE

    Strange, Richard W.; Hough, Michael A.; Antonyuk, Svetlana V.; Hasnain, S. Samar

    2012-01-01

    Copper-zinc superoxide dismutase (SOD) is of fundamental importance to our understanding of oxidative damage. Its primary function is catalysing the dismutation of superoxide to O(2) and H(2)O(2). SOD also reacts with H(2)O(2), leading to the formation of a strong copper-bound oxidant species that can either inactivate the enzyme or oxidise other substrates. In the presence of bicarbonate (or CO(2)) and H(2)O(2), this peroxidase activity is enhanced and produces the carbonate radical. This fr...

  6. Bounds on dark matter interactions with electroweak gauge bosons

    Energy Technology Data Exchange (ETDEWEB)

    Cotta, R. C.; Hewett, J. L.; Le, M. -P.; Rizzo, T. G.

    2013-12-01

    We investigate scenarios in which dark matter interacts with the Standard Model primarily through electroweak gauge bosons. We employ an effective field theory framework wherein the Standard Model and the dark matter particle are the only light states in order to derive model-independent bounds. Bounds on such interactions are derived from dark matter production by weak boson fusion at the LHC, indirect detection searches for the products of dark matter annihilation and from the measured invisible width of the Z 0 . We find that limits on the UV scale, Λ , reach weak scale values for most operators and values of the dark matter mass, thus probing the most natural scenarios in the weakly interacting massive particle dark matter paradigm. Our bounds suggest that light dark matter ( m χ ≲ m Z / 2 or m χ ≲ 100 – 200 GeV , depending on the operator) cannot interact only with the electroweak gauge bosons of the Standard Model, but rather requires additional operator contributions or dark sector structure to avoid overclosing the Universe.

  7. Classical simulations of heavy-ion fusion reactions and weakly ...

    Indian Academy of Sciences (India)

    This model is extended to simulate heavy-ion reactions such as 6Li + 209Bi involving the weakly-bound projectile considered as a weakly-bound cluster of deuteron and 4He nuclei, thus, simulating a 3-body system in 3S-CMD model. All the essential features of breakup reactions, such as complete fusion, incomplete fusion ...

  8. Structural and immunochemical homologies between foxtail millet glutelin 60 kDa and starch granule-bound starch synthase proteins from rice, barley, corn and wheat grains.

    Science.gov (United States)

    Takumi, K; Udaka, J; Kimoto, M; Koga, T; Tsuji, H

    2000-04-01

    Foxtail millet glutelin 60 kDa (MG60) was purified by preparative SDS-PAGE, and the N-terminal amino acid sequence was determined within 20 residues. The result demonstrated that the primary structure at N-terminal of MG60 was almost identical to those of the granule-bound starch synthase (GBSS) proteins from rice, barley, corn, wheat and potato. The existence of common epitopes among MG60 and GBSS proteins from these starch-storing cereals were corroborated by immunoblot analysis using antisera raised against MG60. These facts strongly suggest a close relationship between MG60-like glutelins and GBSS proteins.

  9. Crystal Structure of the Zinc-dependent MarR Family Transcriptional Regulator AdcR in the Zn(II)-bound State

    OpenAIRE

    Guerra, Alfredo J.; Dann, Charles E.; Giedroc, David P.

    2011-01-01

    S. pneumoniae adhesin competence regulator (AdcR), the first metal dependent member of the MarR family of proteins, represses the transcription of a high affinity zinc-specific uptake transporter, a group of surface antigen zinc-binding pneumococcal histidine triad proteins (PhtA, PhtB, PhtD and PhtE) and an AdcA homologue (AdcAII). The 2.0 Å resolution structure of Zn(II)-bound AdcR reveals a highly helical two-fold symmetric dimer with two distinct metal binding sites per protomer. Zn(II) i...

  10. Quasi-bounded sets

    Directory of Open Access Journals (Sweden)

    Jan Kucera

    1990-01-01

    Full Text Available It is proved in [1] & [2] that a set bounded in an inductive limit E=indlim En of Fréchet spaces is also bounded in some En iff E is fast complete. In the case of arbitrary locally convex spaces En every bounded set in a fast complete indlim En is quasi-bounded in some En, though it may not be bounded or even contained in any En. Every bounded set is quasi-bounded. In a Fréchet space every quasi-bounded set is also bounded.

  11. The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions.

    Science.gov (United States)

    Deng, Xiaoyi; Matthews, David; Rathod, Pradipsinh K; Phillips, Margaret A

    2015-05-01

    Plasmodium species are protozoan parasites that are the causative agent of malaria. Malaria is a devastating disease, and its treatment and control have been hampered by the propensity of the parasite to become drug-resistant. Dihydroorotate dehydrogenase (DHODH) has been identified as a promising new target for the development of antimalarial agents. Here, the X-ray structure of P. falciparum DHODH bound to a potent and selective N-phenylbenzamide-based inhibitor (DSM59) is described at 2.3 Å resolution. The structure elucidates novel binding-site interactions and shows how conformational flexibility of the enzyme leads to the ability to bind diverse chemical structures with high affinity. This information provides new insight into the design of high-affinity DHODH inhibitors for the treatment of malaria.

  12. Removal of tightly bound ADP induces distinct structural changes of the two tryptophan-containing regions of the ncd motor domain.

    Science.gov (United States)

    Morii, Hisayuki; Shimizu, Takashi; Mizuno, Naoko; Edamatsu, Masaki; Ogawa, Kazuo; Shimizu, Youské; Toyoshima, Yoko Y

    2005-07-01

    ncd is a molecular motor belonging to the kinesin superfamily. In solution, it is a homo-dimer of a 700 amino acid polypeptide. The C-terminus of each polypeptide forms a globular domain of about 40 kDa, the motor domain with ATPase activity. The ATPase site of the motor domain of kinesin family members, including ncd, binds ADP tightly, the release of which is facilitated by microtubules during the mechanochemical ATPase cycle. Previously, we studied the spectroscopic characteristics of the ncd motor domain, focusing on interactions of the transition-moment-dipoles between ADP and aromatic amino acid side chains using circular dichroism (CD) spectroscopy. In the present study, we generated several ncd motor domain mutants. In each, a tryptophanyl or specific tyrosyl residue was mutated. We found that Trp370 and Tyr442, the latter of which stacks directly with the adenine moiety of bound ADP, caused the bound ADP to exhibit peculiar CD signals. In addition, fluorescence measurements revealed that Trp370, but not Trp473, was responsible for the emission intensity change depending on the presence or absence of bound ADP. This fluorescence result implies that the structural change induced at the ADP-binding site (on the release of the ADP) is transmitted to the region that includes Trp370, which is relatively close to the ADP-binding site but not in direct contact with the ADP-binding region. In contrast, Trp473 in the region that is in contact with the alpha-helical coiled coil stalk did not experience the structural changes caused on removal of ADP. The distinct behavior of these two tryptophanyl residues suggests that the ncd motor domain has a bifacial architecture made up of a relatively deformable side including the nucleotide binding site and a more rigid one.

  13. Competing bounds on the present-day time variation of fundamental constants

    Science.gov (United States)

    Dent, Thomas; Stern, Steffen; Wetterich, Christof

    2009-04-01

    We compare the sensitivity of a recent bound on time variation of the fine structure constant from optical clocks with bounds on time-varying fundamental constants from atomic clocks sensitive to the electron-to-proton mass ratio, from radioactive decay rates in meteorites, and from the Oklo natural reactor. Tests of the weak equivalence principle also lead to comparable bounds on present variations of constants. The “winner in sensitivity” depends on what relations exist between the variations of different couplings in the standard model of particle physics, which may arise from the unification of gauge interactions. Weak equivalence principle tests are currently the most sensitive within unified scenarios. A detection of time variation in atomic clocks would favor dynamical dark energy and put strong constraints on the dynamics of a cosmological scalar field.

  14. Near-horizon Structure of Escape Zones of Electrically Charged Particles around Weakly Magnetized Rotating Black Hole

    Science.gov (United States)

    Kopáček, Ondřej; Karas, Vladimír

    2018-01-01

    An interplay of magnetic fields and gravitation drives accretion and outflows near black holes. However, a specific mechanism is still a matter of debate; it is very likely that different processes dominate under various conditions. In particular, for the acceleration of particles and their collimation in jets, an ordered component of the magnetic field seems to be essential. Here we discuss the role of large-scale magnetic fields in transporting the charged particles and dust grains from the bound orbits in the equatorial plane of a rotating (Kerr) black hole and the resulting acceleration along trajectories escaping the system in a direction parallel to the symmetry axis (perpendicular to the accretion disk). We consider a specific scenario of destabilization of circular geodesics of initially neutral matter by charging (e.g., due to photoionization). Some particles may be set on escaping trajectories and attain relativistic velocity. The case of charged particles differs from charged dust grains by their charge-to-mass ratio, but the acceleration mechanism operates in a similar manner. It appears that the chaotic dynamics controls the outflow and supports the formation of near-horizon escape zones. We employ the technique of recurrence plots to characterize the onset of chaos in the outflowing medium. We investigate the system numerically and construct the basin-boundary plots, which show the location and the extent of the escape zones. The effects of black hole spin and magnetic field strength on the formation and location of escape zones are discussed, and the maximal escape velocity is computed.

  15. Bounding the space of holographic CFTs with chaos

    Energy Technology Data Exchange (ETDEWEB)

    Perlmutter, Eric [Department of Physics, Princeton University,Jadwin Hall, Princeton, NJ 08544 (United States)

    2016-10-13

    Thermal states of quantum systems with many degrees of freedom are subject to a bound on the rate of onset of chaos, including a bound on the Lyapunov exponent, λ{sub L}≤2π/β. We harness this bound to constrain the space of putative holographic CFTs and their would-be dual theories of AdS gravity. First, by studying out-of-time-order four-point functions, we discuss how λ{sub L}=2π/β in ordinary two-dimensional holographic CFTs is related to properties of the OPE at strong coupling. We then rule out the existence of unitary, sparse two-dimensional CFTs with large central charge and a set of higher spin currents of bounded spin; this implies the inconsistency of weakly coupled AdS{sub 3} higher spin gravities without infinite towers of gauge fields, such as the SL(N) theories. This fits naturally with the structure of higher-dimensional gravity, where finite towers of higher spin fields lead to acausality. On the other hand, unitary CFTs with classical W{sub ∞}[λ] symmetry, dual to 3D Vasiliev or hs[λ] higher spin gravities, do not violate the chaos bound, instead exhibiting no chaos: λ{sub L}=0. Independently, we show that such theories violate unitarity for |λ|>2. These results encourage a tensionless string theory interpretation of the 3D Vasiliev theory.

  16. Dependence of myosin-ATPase on structure bound creatine kinase in cardiac myfibrils from rainbow trout and freshwater turtle

    DEFF Research Database (Denmark)

    Haagensen, L.; Jensen, D.H.; Gesser, Hans

    2008-01-01

    The influence of myofibrillar creatine kinase on the myosin-ATPase activity was examined in cardiac ventricular myofibrils isolated from rainbow trout (Oncorhynchus mykiss) and freshwater turtle (Trachemys scripta). The ATPase rate was assessed by recording the rephosphorylation of ADP by the pyr......The influence of myofibrillar creatine kinase on the myosin-ATPase activity was examined in cardiac ventricular myofibrils isolated from rainbow trout (Oncorhynchus mykiss) and freshwater turtle (Trachemys scripta). The ATPase rate was assessed by recording the rephosphorylation of ADP...... by the pyruvate kinase reaction alone or together with the amount of creatine formed, when myofibrillar bound creatine kinase was activated with phosphocreatine. The steady-state concentration of ADP in the solution was varied through the activity of pyruvate kinase added to the solution. For rainbow trout...... myofibrils at a high pyruvate kinase activity, creatine kinase competed for ADP but did not influence the total ATPase activity. When the ADP concentration was elevated within the physiological range by lowering the pyruvate kinase activity, creatine kinase competed efficiently and increased the ATPase...

  17. The first X-ray crystal structure of the glucocorticoid receptor bound to a non-steroidal agonist

    Energy Technology Data Exchange (ETDEWEB)

    Madauss, Kevin P.; Bledsoe, Randy K.; Mclay, Iain; Stewart, Eugene L.; Uings, Iain J.; Weingarten, Gordon; Williams, Shawn P. (GSKNC); (GSK)

    2009-07-23

    The amino-pyrazole 2,6-dichloro-N-ethyl benzamide 1 is a selective GR agonist with dexamethasone-like in vitro potency. Its X-ray crystal structure in the GR LBD (Glucocorticoid ligand-binding domain) is described and compared to other reported structures of steroidal GR agonists in the GR LBD (3E7C).

  18. Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.

    Science.gov (United States)

    Pallan, Pradeep S; Prakash, Thazha P; de Leon, Arnie R; Egli, Martin

    2016-09-27

    RNase H1 cleaves the RNA strand of RNA:DNA hybrids. Replacement of RNA 2'-hydroxyls by fluorine (FRNA) is commonly used to stabilize aptamers and siRNAs. However, FRNA:DNA hybrids fail to elicit RNase H activity. The underlying reasons are unclear, as 2'-OH groups are not directly involved in cleavage. We determined the crystal structure of Bacillus halodurans RNase H bound to a FRNA:DNA hybrid. The structure points to dynamic (slippage of the FRNA:DNA hybrid relative to the enzyme), geometric (different curvatures of FRNA:DNA and RNA:DNA hybrids), and electronic reasons (Mg(2+) absent from the active site of the FRNA:DNA complex) for the loss of RNaseH activity.

  19. Far-Infrared Spectroscopy of Weakly Bound Hydrated Cluster Molecules

    DEFF Research Database (Denmark)

    Andersen, Jonas

    -sized molecular clusters with water by means of far-infrared and terahertz neon matrix isolation spectroscopy. The embedding of non-covalent cluster molecules in solid cryogenic neon matrices at 2.8 K ensures a high sensitivity for direct spectroscopic observations of the large-amplitude intermolecular...

  20. Experimental observation of structures with subtle balance between strong hydrogen bond and weak n → π(*) interaction: Gas phase laser spectroscopy of 7-azaindole⋯fluorosubstituted pyridines.

    Science.gov (United States)

    Singh, Santosh K; Vaishnav, Jamuna K; Das, Aloke

    2016-09-14

    In this study, interplay between a strong hydrogen bond and a very weak n → π(*) interaction has been probed through experiment for the first time. We have used resonant 2-photon ionization, Infrared-ultraviolet double resonance spectroscopy, and quantum chemistry calculation to determine the structures of 7-azaindole⋯2,6-difluoropyridine and 7-azaindole⋯2,3,5,6-tetrafluororpyridine complexes, which are stabilized by both hydrogen bonding and n → π(*) interaction. The structures of the complexes studied in the present work have been compared with the double hydrogen bonded (N-H⋯N and C-H⋯N) planar structure of 7-azaindole⋯2-fluoropyridine. It has been found that the strength of the N-H⋯N hydrogen bond in the 7-azaindole⋯2,6-substituted fluoropyridines is affected due to several factors. The main reason for huge reduction in the strength of this N-H⋯N hydrogen bond in these complexes is due to loss of the C-H⋯N hydrogen bond, through substitution of fluorine atoms in 2 and 6 positions, which induces major structural changes by bending the hydrogen bond and introducing the n → π(*) interaction. Effect of fluorination as well as presence of the n → π(*) interaction in these complexes also contributes to the reduction of the strength of the N-H⋯N interaction. Although it is difficult to quantify the role of the n → π(*) interaction to affect the strength of the hydrogen bond, observation of the structures, where a strong hydrogen bond and a weak n → π(*) interaction co-exist, is confirmed.

  1. Structure and stability of noble gas bound EX3+ compounds (E = C, Ge, Sn, Pb; X = H, F, Cl, Br).

    Science.gov (United States)

    Pan, Sudip; Moreno, Diego; Ghosh, Sreyan; Chattaraj, Pratim K; Merino, Gabriel

    2016-01-15

    It has been analyzed at the MP2/def2-QZVPPD level whether EX3+ (E = C-Pb; X = H, F-Br) can bind noble gas atoms. Geometrical and electronic structures, dissociation energy values, thermochemical parameters, natural bond order, electron density, and energy decomposition analyses highlight the possibility of such noble gas bound EX3+ compounds. Except He and Ne, the other heavier congeners of this family make quite strong bonds with E. In fact, the dissociations of Ar-Rn bound analogues turn out to be endergonic in nature at 298 K, except in the cases of ArGe Cl3+, Ar/KrGeBr3+, and ArSnBr3+. GeH3+ and EF3+ (E = Ge-Pb) can even bind two Ng atoms with reasonably high dissociation energy. As the pz orbital of the E center in EX3+ plays a crucial role in its binding with the noble gas atoms, the effect of the π back-bonding causing X → E electron transfer ought to be properly understood. Due to the larger back-donation, the Ng binding ability of EX3+ gradually decreases along F to Br. EH2+ and the global minimum HE(+…) H2 (E = Sn, Pb) complexes are also able to bind Ar-Rn atoms quite effectively. The NgE bonds in Ar-Rn bound CH3+, GeH3+, and EF3+ (E = Ge-Pb) and Xe/RnE bonds in NgECl3+ and NgEBr3+ (E = Ge, Sn) are mainly of covalent type. © 2015 Wiley Periodicals, Inc.

  2. Weak lensing with GEST

    Science.gov (United States)

    Rhodes, J. D.; Bennett, D. P.; Kaiser, N.

    2001-12-01

    Weak lensing by large-scale structure (cosmic shear) provides an opportunity to directly observe the dark matter in the universe. Current ground-based and space-based surveys have demonstrated the efficacy of this technique in determining the mass distribution and thus placing constraints on cosmological parameters such as Ω m, σ 8, and the bias parameter b. Current surveys have been hampered by the comparatively low resolution of ground-based telescopes and the small field of view of HST. To make significant progress in this field, wide field space-based surveys are needed. The Galactic Exoplanet Survey Telescope (GEST) will be able to provide 500- 1000 sqare degrees with a resolution of better than 0.2 arcseconds in multiple filters. This will make it an ideal instrument for a weak lensing survey.

  3. On weakly D-differentiable operators

    DEFF Research Database (Denmark)

    Christensen, Erik

    2016-01-01

    Let DD be a self-adjoint operator on a Hilbert space HH and aa a bounded operator on HH. We say that aa is weakly DD-differentiable, if for any pair of vectors ξ,ηξ,η from HH the function 〈eitDae−itDξ,η〉〈eitDae−itDξ,η〉 is differentiable. We give an elementary example of a bounded operator aa...

  4. Planning, Plumbing, or Posturing? Explaining the Weakness of Human Resource Development Structures and Policies in South Africa

    Science.gov (United States)

    Allais, Stephanie; Marock, Carmel; Ngcwangu, Siphelo

    2017-01-01

    In South Africa, a national peak structure, the Human Resource Development Council, led by the Deputy President and consisting of key Cabinet Ministers, senior leaders from organised labour and business, community representatives, professional bodies and experts from research and higher education, was established to enable high-level coordination…

  5. Experimental data from irradiation of physical detectors disclose weaknesses in basic assumptions of the δ ray theory of track structure

    DEFF Research Database (Denmark)

    Olsen, K. J.; Hansen, Jørgen-Walther

    1985-01-01

    The applicability of track structure theory has been tested by comparing predictions based on the theory with experimental high-LET dose-response data for an amino acid alanine and a nylon based radiochromic dye film radiation detector. The linear energy transfer LET, has been varied from 28...

  6. Revelation of endogenously bound Fe{sup 2+} ions in the crystal structure of ferritin from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Thiruselvam, Viswanathan [Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India); Sivaraman, Padavattan [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Kumarevel, Thirumananseri, E-mail: kumarevel.thirumananseri@riken.jp [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan); Ponnuswamy, Mondikalipudur Nanjappagounder, E-mail: mnpsy2004@yahoo.com [Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India)

    2014-10-24

    Highlights: • Crystal structure of ferritin was determined. • Endogenously expressed iron’s were identified. • Binuclear iron sites were observed at A and B active sites. - Abstract: Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites. The protein was purified and characterized by MALDI-TOF and N-terminal amino acid sequencing. The crystal belongs to I4 space group and it diffracted up to 2.5 Å. The structural analysis suggested that it crystallizes as hexamer and confirmed that it happened to be the first report of endogenously expressed Fe ions incorporated in both the A and B sites, situated in between the helices.

  7. Experimental evidence suggesting slow or weak response of nematode community structure to a large suspension-feeder

    Science.gov (United States)

    Austen, Melanie C.; Thrush, Simon F.

    2001-08-01

    An experiment was carried out in a shallow, subtidal site in Mahurangi Harbour, New Zealand, to examine the effects of the large pinnid bivalve Atrina zelandica on benthic communities. Early on in the experiment, after 47 days, samples were taken specifically to examine the response of the meiofauna communities and particularly nematode assemblage structure to the presence of different densities of Atrina. Dead shell treatments were included in the experiment to discriminate between the effects of the physical presence of Atrina and the effects of their biological activity. There were no observable effects of either different densities of Atrina or of the dead shell treatments on nematode assemblage structure. There were no consistent treatment-related effects on community structure of meiofaunal major taxa. A previous field study had shown that nematode communities differed inside and outside dense natural patches of Atrina. Data manipulations combined with the use of ANOSIM show that the experimental design was sufficiently powerful to have detected these differences if they had occurred in the experiment. Speculations on the current lack of the experimental effect include: (1) the meiofauna communities in field sites containing high densities of Atrina are structured by other factors (which may be coincidentally attractive to the Atrina) rather than by the presence or activities of the Atrina themselves; and (2) Atrina in natural patches may condition the sediment in some way that can affect the meiofauna, perhaps through alteration in flow regime which could affect sediment chemistry or through changes in biodeposit levels within the sediment, but these habitat alterations or the reaction of meiofauna to them do not occur within the 47-day time scale of our experiment.

  8. Quercetin modulates activities of Taiwan cobra phospholipase A2 via its effects on membrane structure and membrane-bound mode of phospholipase A2.

    Science.gov (United States)

    Chiou, Yi-Ling; Lin, Shinne-Ren; Hu, Wan-Ping; Chang, Long-Sen

    2012-06-01

    The goal of the present study is to elucidate the mechanism of quercetin on modulating Naja naja atra phospholipase A2 (PLA2) activities. Sphingomyelin inhibited PLA2 enzymatic activity and membrane-damaging activity against egg yolk phosphatidylcholine (EYPC), while cholesterol and quercetin abrogated the sphingomeyelin inhibitory effect. Quercetin incorporation led to a reduction in PLA2 enzymatic activity and membrane-damaging activity toward EYPC/sphingomyelin/cholesterol vesicles. Both cholesterol and quercetin increased detergent resistance and reduced membrane fluidity of EYPC/sphingomyelin vesicles. Quercetin reduced detergent insolubility but increased ordered lipid packing of EYPC/sphingomyelin/cholesterol vesicles. Acrylamide quenching studies and trinitrophenylation of Lys residues revealed that quercetin altered the membrane-bound mode of PLA2 differently upon absorption onto the membrane bilayers of different lipid compositions. However, 8-anilinonaphthalene sulphonate-binding assay revealed that quercetin marginally affected the interaction between active site of PLA2 with phospholipid vesicles. Collectively, our data indicate that membrane-inserted quercetin modulates PLA2 interfacial activity and membrane-damaging activity via its effects on membrane structure and membrane-bound mode of PLA2.

  9. Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution

    Science.gov (United States)

    Quade, Nick; Boehringer, Daniel; Leibundgut, Marc; van den Heuvel, Joop; Ban, Nenad

    2015-07-01

    Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.

  10. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA

    DEFF Research Database (Denmark)

    Andersen, Christian Brix Folsted; Ballut, Lionel; Johansen, Jesper Sanderhoff

    2006-01-01

    In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric e...

  11. Crystal structure of the active form of native human thymidylate synthase in the absence of bound substrates.

    Science.gov (United States)

    Deschamps, P; Réty, S; Bareille, J; Leulliot, N

    2017-06-01

    Human thymidylate synthase (hTS) provides the sole de novo intracellular source of thymidine 5'-monophosphate (dTMP). hTS is required for DNA replication prior to cell division, making it an attractive target for anticancer chemotherapy and drug discovery. hTS binds 2'-deoxyuridine 5'-monophosphate (dUMP) and the folate co-substrate N 5 ,N 10 -methylenetetrahydrofolate (meTHF) in a pocket near the catalytic residue Cys195. The catalytic loop, which is composed of amino-acid residues 181-197, can adopt two distinct conformations related by a 180° rotation. In the active conformation Cys195 is close to the active site, while in the inactive conformation it is rotated and Cys195 is too distant from the active site for catalysis. Several hTS structures, either native or engineered, have been solved in the active conformation in complex with ligands or inhibitors and at different salt concentrations. However, apo hTS structures have been solved in an inactive conformation in high-salt and low-salt conditions (PDB entries 1ypv, 4h1i, 4gyh, 3egy and 3ehi). Here, the structure of apo hTS crystallized in the active form with sulfate ions coordinated by the arginine residue that binds dUMP is reported.

  12. The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins.

    Science.gov (United States)

    López-Carrasco, Amparo; Flores, Ricardo

    2017-07-01

    Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.

  13. Structure of the Epstein-Barr virus gp42 protein bound to the MHC class II recepter HLA-DR1

    Energy Technology Data Exchange (ETDEWEB)

    Mullen, M.; Haan, K.M.; Longnecker, R.; Jardetzky, T.

    2010-03-08

    Epstein-Barr virus (EBV) causes infectious mononucleosis, establishes long-term latent infections, and is associated with a variety of human tumors. The EBV gp42 glycoprotein binds MHC class II molecules, playing a critical role in infection of B lymphocytes. EBV gp42 belongs to the C-type lectin superfamily, with homology to NK receptors of the immune system. We report the crystal structure of gp42 bound to the human MHC class II molecule HLA-DR1. The gp42 binds HLA-DR1 using a surface site that is distinct from the canonical lectin and NK receptor ligand binding sites. At the canonical ligand binding site, gp42 forms a large hydrophobic groove, which could interact with other ligands necessary for EBV entry, providing a mechanism for coupling MHC recognition and membrane fusion.

  14. Crystal structure of the NADP+and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.

    Science.gov (United States)

    Yoneda, Kazunari; Sakuraba, Haruhiko; Araki, Tomohiro; Ohshima, Toshihisa

    2018-01-20

    A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C. The enzyme showed substantial reactivity towards D-serine, in addition to L-serine. Two different crystal structures of P. calidifontis L-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP + /sulfate ion at 1.18 Å and the structure in complex with NADP + /L-tartrate (substrate analog) at 1.57 Å. The fold of the catalytic domain showed similarity with that of Ps. aeruginosa L-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. This is the first description of the structure of the novel type of L-SerDH with bound NADP + and substrate analog, and it provides new insight into the substrate binding mechanism of L-SerDH. The results obtained here may be very informative for the creation of L- or D-serine-specific SerDH by protein engineering.

  15. Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the alpha-subunit.

    Science.gov (United States)

    Sazinsky, Matthew H; Lippard, Stephen J

    2005-04-27

    The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot. To understand better the functions of the cavities and to investigate how an enzyme designed for methane hydroxylation can also accommodate larger substrates such as octane, methylcubane, and trans-1-methyl-2-phenylcyclopropane, MMOH crystals were soaked with an assortment of different alcohols and their X-ray structures were solved to 1.8-2.4 A resolution. The product analogues localize to cavities 1-3 and delineate a path of product exit and/or substrate entrance from the active site to the surface of the protein. The binding of the alcohols to a position bridging the two iron atoms in cavity 1 extends and validates previous crystallographic, spectroscopic, and computational work indicating this site to be where substrates are hydroxylated and products form. The presence of these alcohols induces perturbations in the amino acid side-chain gates linking pairs of cavities, allowing for the formation of a channel similar to one observed in ToMOH. Upon binding of 6-bromohexan-1-ol, the pi helix formed by residues 202-211 in helix E of the alpha-subunit is extended through residue 216, changing the orientations of several amino acid residues in the active site cavity. This remarkable secondary structure rearrangement in the four-helix bundle has several mechanistic implications for substrate accommodation and the function of the effector protein, MMOB.

  16. Sound velocity bound and neutron stars.

    Science.gov (United States)

    Bedaque, Paulo; Steiner, Andrew W

    2015-01-23

    It has been conjectured that the velocity of sound in any medium is smaller than the velocity of light in vacuum divided by sqrt[3]. Simple arguments support this bound in nonrelativistic and/or weakly coupled theories. The bound has been demonstrated in several classes of strongly coupled theories with gravity duals and is saturated only in conformal theories. We point out that the existence of neutron stars with masses around two solar masses combined with the knowledge of the equation of state of hadronic matter at "low" densities is in strong tension with this bound.

  17. Crystal structure of the Hendra virus attachment G glycoprotein bound to a potent cross-reactive neutralizing human monoclonal antibody.

    Directory of Open Access Journals (Sweden)

    Kai Xu

    Full Text Available The henipaviruses, represented by Hendra (HeV and Nipah (NiV viruses are highly pathogenic zoonotic paramyxoviruses with uniquely broad host tropisms responsible for repeated outbreaks in Australia, Southeast Asia, India and Bangladesh. The high morbidity and mortality rates associated with infection and lack of licensed antiviral therapies make the henipaviruses a potential biological threat to humans and livestock. Henipavirus entry is initiated by the attachment of the G envelope glycoprotein to host cell membrane receptors. Previously, henipavirus-neutralizing human monoclonal antibodies (hmAb have been isolated using the HeV-G glycoprotein and a human naïve antibody library. One cross-reactive and receptor-blocking hmAb (m102.4 was recently demonstrated to be an effective post-exposure therapy in two animal models of NiV and HeV infection, has been used in several people on a compassionate use basis, and is currently in development for use in humans. Here, we report the crystal structure of the complex of HeV-G with m102.3, an m102.4 derivative, and describe NiV and HeV escape mutants. This structure provides detailed insight into the mechanism of HeV and NiV neutralization by m102.4, and serves as a blueprint for further optimization of m102.4 as a therapeutic agent and for the development of entry inhibitors and vaccines.

  18. Crystal structure of the Hendra virus attachment G glycoprotein bound to a potent cross-reactive neutralizing human monoclonal antibody.

    Science.gov (United States)

    Xu, Kai; Rockx, Barry; Xie, Yihu; DeBuysscher, Blair L; Fusco, Deborah L; Zhu, Zhongyu; Chan, Yee-Peng; Xu, Yan; Luu, Truong; Cer, Regina Z; Feldmann, Heinz; Mokashi, Vishwesh; Dimitrov, Dimiter S; Bishop-Lilly, Kimberly A; Broder, Christopher C; Nikolov, Dimitar B

    2013-01-01

    The henipaviruses, represented by Hendra (HeV) and Nipah (NiV) viruses are highly pathogenic zoonotic paramyxoviruses with uniquely broad host tropisms responsible for repeated outbreaks in Australia, Southeast Asia, India and Bangladesh. The high morbidity and mortality rates associated with infection and lack of licensed antiviral therapies make the henipaviruses a potential biological threat to humans and livestock. Henipavirus entry is initiated by the attachment of the G envelope glycoprotein to host cell membrane receptors. Previously, henipavirus-neutralizing human monoclonal antibodies (hmAb) have been isolated using the HeV-G glycoprotein and a human naïve antibody library. One cross-reactive and receptor-blocking hmAb (m102.4) was recently demonstrated to be an effective post-exposure therapy in two animal models of NiV and HeV infection, has been used in several people on a compassionate use basis, and is currently in development for use in humans. Here, we report the crystal structure of the complex of HeV-G with m102.3, an m102.4 derivative, and describe NiV and HeV escape mutants. This structure provides detailed insight into the mechanism of HeV and NiV neutralization by m102.4, and serves as a blueprint for further optimization of m102.4 as a therapeutic agent and for the development of entry inhibitors and vaccines.

  19. X-ray crystal structure of teicoplanin A₂-2 bound to a catalytic peptide sequence via the carrier protein strategy.

    Science.gov (United States)

    Han, Sunkyu; Le, Binh V; Hajare, Holly S; Baxter, Richard H G; Miller, Scott J

    2014-09-19

    We report the X-ray crystal structure of a site-selective peptide catalyst moiety and teicoplanin A2-2 complex. The expressed protein ligation technique was used to couple T4 lysozyme (T4L) and a synthetic peptide catalyst responsible for the selective phosphorylation of the N-acetylglucosamine sugar in a teicoplanin A2-2 derivative. The T4L-Pmh-dPro-Aib-dAla-dAla construct was crystallized in the presence of teicoplanin A2-2. The resulting 2.3 Å resolution protein-peptide-teicoplanin complex crystal structure revealed that the nucleophilic nitrogen of N-methylimidazole in the Pmh residue is in closer proximity (7.6 Å) to the N-acetylglucosamine than the two other sugar rings present in teicoplanin (9.3 and 20.3 Å, respectively). This molecular arrangement is consistent with the observed selectivity afforded by the peptide-based catalyst when it is applied to a site-selective phosphorylation reaction involving a teicoplanin A2-2 derivative.

  20. HIV-1 Reverse Transcriptase Structure with RNase H Inhibitor dihydroxy benzoyl naphthyl Hydrazone Bound at a Novel Site

    Energy Technology Data Exchange (ETDEWEB)

    Himmel,D.; Sarafianos, S.; Dharmasena, S.; Hossain, M.; McCoy-Simandle, K.; Ilina, T.; Clark, A.; Knight, J.; Julias, J.; et al.

    2007-01-01

    The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new lead compounds that target novel binding sites are needed. We have determined the 3.15 {angstrom} resolution crystal structure of HIV-1 reverse transcriptase (RT) complexed with dihydroxy benzoyl naphthyl hydrazone (DHBNH), an HIV-1 RT RNase H (RNH) inhibitor (RNHI). DHBNH is effective against a variety of drug-resistant HIV-1 RT mutants. While DHBNH has little effect on most aspects of RT-catalyzed DNA synthesis, at relatively high concentrations it does inhibit the initiation of RNA-primed DNA synthesis. Although primarily an RNHI, DHBNH binds >50 {angstrom} away from the RNH active site, at a novel site near both the polymerase active site and the non-nucleoside RT inhibitor (NNRTI) binding pocket. When DHBNH binds, both Tyr181 and Tyr188 remain in the conformations seen in unliganded HIV-1 RT. DHBNH interacts with conserved residues (Asp186, Trp229) and has substantial interactions with the backbones of several less well-conserved residues. On the basis of this structure, we designed substituted DHBNH derivatives that interact with the NNRTI-binding pocket. These compounds inhibit both the polymerase and RNH activities of RT.

  1. Structures of C-mannosylated anti-adhesives bound to the type 1 fimbrial FimH adhesin

    Directory of Open Access Journals (Sweden)

    Jerome de Ruyck

    2016-05-01

    Full Text Available Selective inhibitors of the type 1 fimbrial adhesin FimH are recognized as attractive alternatives for antibiotic therapies and prophylaxes against Escherichia coli infections such as urinary-tract infections. To construct these inhibitors, the α-d-mannopyranoside of high-mannose N-glycans, recognized with exclusive specificity on glycoprotein receptors by FimH, forms the basal structure. A hydrophobic aglycon is then linked to the mannose by the O1 oxygen inherently present in the α-anomeric configuration. Substitution of this O atom by a carbon introduces a C-glycosidic bond, which may enhance the therapeutic potential of such compounds owing to the inability of enzymes to degrade C-glycosidic bonds. Here, the first crystal structures of the E. coli FimH adhesin in complex with C-glycosidically linked mannopyranosides are presented. These findings explain the role of the spacer in positioning biphenyl ligands for interactions by means of aromatic stacking in the tyrosine gate of FimH and how the normally hydrated C-glycosidic link is tolerated. As these new compounds can bind FimH, it can be assumed that they have the potential to serve as potent new antagonists of FimH, paving the way for the design of a new family of anti-adhesive compounds against urinary-tract infections.

  2. Initiation and development of the Kivu rift segment in Central Africa by reactivating un-favorably oriented structural weaknesses

    Science.gov (United States)

    Delvaux, Damien; Smets, Benoît

    2015-04-01

    The Kivu rift region forms the central segment of the western branch of the East African rift system, between the northern termination of the Tanganyika rift and the southern extension of the Edward-George rift. Its structure and geological evolution has been revised in the light of a compilation of existing data on earthquake epicenters, focal depth, focal mechanisms, thermal springs and neotectonic faults. It has long been shown that the link between the Kivu rift basin and the Northern termination of the Tanganyika rift basin forms an accommodation zone in which the Rusizi tectonic depression occupies a central place (Ebinger, 1989). In addition, our compilation suggests that the NNE-trending Kivu rift basin and the N-S northern half of the Tanganyika rift basin initiated as separated, partly overlapping and differently oriented basins. The orientation and development of the Kivu rift basin was controlled by an inferred Mid-Proterozoic crustal shear zone and a Pan-African reverse fault front. It was not optimally oriented with the general (first-order) stress field characterized by roughly E-W extension. In a later stage, the more optimally N-S oriented North Tanganyika basin progressed towards the North and connected to Kivu rift in its middle in a region now occupied by the town of Bukavu. This accommodation zone is marked by Quaternary volcanism, warm thermal springs, frequent and relatively shallow seismicity. The southwestern part of the Kivu rift became progressively abandoned but it is still seismically active and hosts a number of warm thermal springs. This particular architecture influences the present-day stress field. This work is a contribution to the Belgian GeoRisCA project. Ebinger, C.J. 1989. Geometric and kinematic development of border faults and accommodation zones, Kivu-Rusizi Rift, Africa. Tectonics, 8, 117-133

  3. Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate.

    Science.gov (United States)

    Ababou, Abdessamad; Koronakis, Vassilis

    2016-01-01

    Gram-negative bacteria such as E. coli use tripartite efflux pumps such as AcrAB-TolC to expel antibiotics and noxious compounds. A key feature of the inner membrane transporter component, AcrB, is a short stretch of residues known as the gate/switch loop that divides the proximal and distal substrate binding pockets. Amino acid substitutions of the gate loop are known to decrease antibiotic resistance conferred by AcrB. Here we present two new AcrB gate loop variants, the first stripped of its bulky side chains, and a second in which the gate loop is removed entirely. By determining the crystal structures of the variant AcrB proteins in the presence and absence of erythromycin and assessing their ability to confer erythromycin tolerance, we demonstrate that the gate loop is important for AcrB export activity but is not required for erythromycin binding.

  4. Lower antigen site density and weak D immunogenicity cannot be explained by structural genomic abnormalities or regulatory defects of the RHD gene

    NARCIS (Netherlands)

    Beckers, E. A.; Faas, B. H.; Ligthart, P.; Overbeeke, M. A.; von dem Borne, A. E.; van der Schoot, C. E.; van Rhenen, D. J.

    1997-01-01

    The weak D phenotype is characterized serologically by a weak or negative agglutination reaction with polyclonal anti-D in an immediate-spin test. Agglutination is enhanced in the indirect antiglobulin test. Red cells that are typed weak D have a much lower number of apparently complete D antigens

  5. Crystal structures of apo and inhibitor-bound TGFβR2 kinase domain: insights into TGFβR isoform selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Tebben, Andrew J.; Ruzanov, Maxim; Gao, Mian; Xie, Dianlin; Kiefer, Susan E.; Yan, Chunhong; Newitt, John A.; Zhang, Liping; Kim, Kyoung; Lu, Hao; Kopcho, Lisa M.; Sheriff, Steven (BMS)

    2016-04-26

    The cytokine TGF-β modulates a number of cellular activities and plays a critical role in development, hemostasis and physiology, as well as in diseases including cancer and fibrosis. TGF-β signals through two transmembrane serine/threonine kinase receptors: TGFβR1 and TGFβR2. Multiple structures of the TGFβR1 kinase domain are known, but the structure of TGFβR2 remains unreported. Wild-type TGFβR2 kinase domain was refractory to crystallization, leading to the design of two mutated constructs: firstly, a TGFβR1 chimeric protein with seven ATP-site residues mutated to their counterparts in TGFβR2, and secondly, a reduction of surface entropy through mutation of six charged residues on the surface of the TGFβR2 kinase domain to alanines. These yielded apo and inhibitor-bound crystals that diffracted to high resolution (<2 Å). Comparison of these structures with those of TGFβR1 reveal shared ligand contacts as well as differences in the ATP-binding sites, suggesting strategies for the design of pan and selective TGFβR inhibitors.

  6. Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata

    Directory of Open Access Journals (Sweden)

    Sanchari Banerjee

    2016-07-01

    Full Text Available Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

  7. Magnetic field structure in single late-type giants: The weak G-band giant 37 Comae from 2008 to 2011

    Science.gov (United States)

    Tsvetkova, S.; Petit, P.; Konstantinova-Antova, R.; Aurière, M.; Wade, G. A.; Palacios, A.; Charbonnel, C.; Drake, N. A.

    2017-03-01

    Aims: This work studies the magnetic activity of the late-type giant 37 Com. This star belongs to the group of weak G-band stars that present very strong carbon deficiency in their photospheres. The paper is a part of a global investigation into the properties and origin of magnetic fields in cool giants. Methods: We use spectropolarimetric data, which allows the simultaneous measurement of the longitudinal magnetic field Bl, line activity indicators (Hα, Ca II IRT, S-index) and radial velocity of the star, and consequently perform a direct comparison of their time variability. Mean Stokes V profiles are extracted using the least squares deconvolution (LSD) method. One map of the surface magnetic field of the star is reconstructed via the Zeeman Doppler imaging (ZDI) inversion technique. Results: A periodogram analysis is performed on our dataset and it reveals a rotation period of 111 days. We interpret this period to be the rotation period of 37 Com. The reconstructed magnetic map reveals that the structure of the surface magnetic field is complex and features a significant toroidal component. The time variability of the line activity indicators, radial velocity and magnetic field Bl indicates a possible evolution of the surface magnetic structures in the period from 2008 to 2011. For completeness of our study, we use customized stellar evolutionary models suited to a weak G-band star. Synthetic spectra are also calculated to confirm the peculiar abundance of 37 Com. Conclusions: We deduce that 37 Com is a 6.5 M⊙ weak G-band star located in the Hertzsprung gap, whose magnetic activity is probably due to dynamo action. Based on observations obtained at the Télescope Bernard Lyot (TBL, Pic du Midi, France) of the Midi-Pyrénées Observatory which is operated by the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France and Université de Toulouse, and at the Canada-France-Hawaii Telescope (CFHT) which is

  8. Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shenyuan; Long, Brian N.; Boris, Gabriel H.; Chen, Anqi; Ni, Shuisong; Kennedy, Michael A.

    2017-11-10

    K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras–GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.

  9. Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.

    Science.gov (United States)

    Xu, Shenyuan; Long, Brian N; Boris, Gabriel H; Chen, Anqi; Ni, Shuisong; Kennedy, Michael A

    2017-12-01

    K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras-GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.

  10. Structural and enzymatic characterization of Drosophila Dm2-MMP, a membrane-bound matrix metalloproteinase with tissue-specific expression.

    Science.gov (United States)

    Llano, Elena; Adam, Geza; Pendás, Alberto M; Quesada, Víctor; Sánchez, Luis M; Santamariá, Iñigo; Noselli, Stéphane; López-Otín, Carlos

    2002-06-28

    We report the isolation and characterization of a cDNA encoding Dm2-MMP, the second matrix metalloproteinase (MMP) identified in the Drosophila melanogaster genome. The cloned cDNA codes for a polypeptide of 758 residues that displays a domain organization similar to that of other MMPs, including signal peptide, propeptide, catalytic, and hemopexin domains. However, the structure of Dm2-MMP is unique because of the presence of an insertion of 214 amino acids between the catalytic and hemopexin domains that is not present in any of the previously described MMPs. Dm2-MMP also contains a C-terminal extension predicted to form a cleavable glycosylphosphatidylinositol anchor site. Western blot and immunofluorescence analysis of S2 cells transfected with the isolated cDNA confirmed that Dm2-MMP is localized at the cell surface. Production of the catalytic domain of Dm2-MMP in Escherichia coli and analysis of its enzymatic activity revealed that this proteinase cleaves several synthetic peptides used for analysis of vertebrate MMPs. This proteolytic activity was abolished by MMP inhibitors such as BB-94, confirming that the isolated cDNA codes for an enzymatically active metalloproteinase. Reverse transcription-PCR analysis showed that Dm2-MMP is expressed at low levels in all of the developmental stages of Drosophila as well as in adult flies. However, detailed in situ hybridization at the larval stage revealed a strong tissue-specific expression in discrete regions of the brain and eye imaginal discs. According to these results, we propose that Dm2-MMP plays both general proteolytic functions during Drosophila development and in adult tissues and specific roles in eye development and neural tissues through the degradation and remodeling of the extracellular matrix.

  11. Electronic structure of a weakly antiferromagnetically coupled Mn(II)Mn(III) model relevant to manganese proteins: a combined EPR, 55Mn-ENDOR, and DFT study.

    Science.gov (United States)

    Cox, Nicholas; Ames, William; Epel, Boris; Kulik, Leonid V; Rapatskiy, Leonid; Neese, Frank; Messinger, Johannes; Wieghardt, Karl; Lubitz, Wolfgang

    2011-09-05

    An analysis of the electronic structure of the [Mn(II)Mn(III)(μ-OH)-(μ-piv)(2)(Me(3)tacn)(2)](ClO(4))(2) (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-μ-hydroxo bridge, bis-μ-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the Mn(III). All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the (55)Mn-ENDOR constrains the (55)Mn hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the Mn(II) and Mn(III) ions. The large effective hyperfine tensor anisotropy of the Mn(II), a d(5) ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the Mn(III) ion strongly perturbs the zero-field energy levels of the Mn(II)Mn(III) complex. An estimate of the fine structure parameter (d) for the Mn(III) of -4 cm(-1) was made, by assuming the intrinsic anisotropy of the Mn(II) ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the Mn(III) is consistent with the known coordination environment of the Mn(III) ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic

  12. Bound states and the Bekenstein bound

    Energy Technology Data Exchange (ETDEWEB)

    Bousso, Raphael

    2003-10-16

    We explore the validity of the generalized Bekenstein bound, S<= pi M a. We define the entropy S as the logarithm of the number of states which have energy eigenvalue below M and are localized to a flat space region of width alpha. If boundary conditions that localize field modes are imposed by fiat, then the bound encounters well-known difficulties with negative Casimir energy and large species number, as well as novel problems arising only in the generalized form. In realistic systems, however, finite-size effects contribute additional energy. We study two different models for estimating such contributions. Our analysis suggests that the bound is both valid and nontrivial if interactions are properly included, so that the entropy S counts the bound states of interacting fields.

  13. Interplay of superconductivity and electrically controlled band structure in silicene 0- π transitions, φ0-junctions, Majorana bound states, and odd-frequency superconductivity

    Science.gov (United States)

    Kuzmanovski, Dushko; Black-Schaffer, Annica; Linder, Jacob

    Silicene, the Si-atom analog of graphene, is a viable candidate for experimental realization of non-trivial topological phases due to the larger spin-orbit coupling. Also, owing to the buckled structure, it allows for tuning of its various band gaps by an applied electric field. An intriguing prospect is to consider effects due to the interplay between the non-trivial band structure and superconducting correlations in silicene, and to study the external control of such unusual phenomena via an electric field. We demonstrate theoretically that proximity-induced superconductivity in silicene offers the possibility to exert strong quantum ground state control. We show that electrically controlled 0- π transitions occur in Josephson junctions in the presence of an exchange field. We also discover that zigzag-oriented interfaces, featuring intervalley scattering, cause a φ0 state with an applied electric field. Additionally, we demonstrate that Majorana bound states along the silicene edge are tunable via the edge orientation, electric, and in-plane spin exchange fields. Finally, we investigate odd-frequency superconducting pair amplitudes in both bulk silicene, and nanoribbons with two kinds of edges.

  14. The Structure of Dasatinib (BNS-354825) Bound to Activated ABL Kinase Domain Elucidates its Inhibitory Activity Against Imatinib-Resistant ABL Mutants

    Energy Technology Data Exchange (ETDEWEB)

    Tokarski,J.; Newitt, J.; Chang, C.; Cheng, J.; Wittekind, M.; Kiefer, S.; Kish, K.; Lee, F.; Borzilerri, R.; et al.

    2006-01-01

    Chronic myeloid leukemia (CML) is caused by the constitutively activated tyrosine kinase breakpoint cluster (BCR)-ABL. Current frontline therapy for CML is imatinib, an inhibitor of BCR-ABL. Although imatinib has a high rate of clinical success in early phase CML, treatment resistance is problematic, particularly in later stages of the disease, and is frequently mediated by mutations in BCR-ABL. Dasatinib (BMS-354825) is a multitargeted tyrosine kinase inhibitor that targets oncogenic pathways and is a more potent inhibitor than imatinib against wild-type BCR-ABL. It has also shown preclinical activity against all but one of the imatinib-resistant BCR-ABL mutants tested to date. Analysis of the crystal structure of dasatinib-bound ABL kinase suggests that the increased binding affinity of dasatinib over imatinib is at least partially due to its ability to recognize multiple states of BCR-ABL. The structure also provides an explanation for the activity of dasatinib against imatinib-resistant BCR-ABL mutants.

  15. Crystal structures of the DNA-binding domain tetramer of the p53 tumor suppressor family member p73 bound to different full-site response elements.

    Science.gov (United States)

    Ethayathulla, Abdul S; Nguyen, H Thien; Viadiu, Hector

    2013-02-15

    How cells choose between developmental pathways remains a fundamental biological question. In the case of the p53 protein family, its three transcription factors (p73, p63, and p53) each trigger a gene expression pattern that leads to specific cellular pathways. At the same time, these transcription factors recognize the same response element (RE) consensus sequences, and their transactivation of target genes overlaps. We aimed to understand target gene selectivity at the molecular level by determining the crystal structures of the p73 DNA-binding domain (DBD) in complex with full-site REs that vary in sequence. We report two structures of the p73 DBD bound as a tetramer to 20-bp full-site REs based on two distinct quarter-sites: GAACA and GAACC. Our study confirms that the DNA-binding residues are conserved within the p53 family, whereas the dimerization and tetramerization interfaces diverge. Moreover, a conserved lysine residue in loop L1 of the DBD senses the presence of guanines in positions 2 and 3 of the quarter-site RE, whereas a conserved arginine in loop 3 adapts to changes in position 5. Sequence variations in the RE elicit a p73 conformational response that might explain target gene specificity.

  16. Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state.

    Science.gov (United States)

    Guerra, Alfredo J; Dann, Charles E; Giedroc, David P

    2011-12-14

    Streptococcus pneumoniae adhesin competence regulator (AdcR), the first metal-dependent member of the multiple antibiotic resistance regulator (MarR) family of proteins, represses the transcription of a high-affinity zinc-specific uptake transporter, a group of surface antigen zinc-binding pneumococcal histidine triad proteins (PhtA, PhtB, PhtD, and PhtE), and an AdcA homologue (AdcAII). The 2.0 Å resolution structure of Zn(II)-bound AdcR reveals a highly helical two-fold-symmetric dimer with two distinct metal-binding sites per protomer. Zn(II) is tetrahedrally coordinated by E24, H42, H108, and H112 in what defines the primary sensing site in AdcR. Site 2 is a tetracoordinate site whose function is currently unknown. NMR methyl group perturbation experiments reveal that Zn(II) drives a global change in the structure of apo-AdcR that stabilizes a conformation that is compatible with DNA binding. This co-repression mechanism is unprecedented in MarR transcriptional regulators. © 2011 American Chemical Society

  17. Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 Å resolution.

    Science.gov (United States)

    de Silva, Udesh; Zhou, Zhaoli; Brown, Bernard A

    2012-08-01

    Fibrillarin is the key methyltransferase associated with the C/D class of small nuclear ribonucleoproteins (snRNPs) and participates in the preliminary step of pre-ribosomal rRNA processing. This molecule is found in the fibrillar regions of the eukaryotic nucleolus and is involved in methylation of the 2'-O atom of ribose in rRNA. Human fibrillarin contains an N-terminal GAR domain, a central RNA-binding domain comprising an RNP-2-like superfamily consensus sequence and a catalytic C-terminal helical domain. Here, Aeropyrum pernix fibrillarin is described, which is homologous to the C-terminal domain of human fibrillarin. The protein was crystallized with an S-adenosyl-L-methionine (SAM) ligand bound in the active site. The molecular structure of this complex was solved using X-ray crystallography at a resolution of 1.7 Å using molecular replacement with fibrillarin structural homologs. The structure shows the atomic details of SAM and its active-site interactions; there are a number of conserved residues that interact directly with the cofactor. Notably, the adenine ring of SAM is stabilized by π-π interactions with the conserved residue Phe110 and by electrostatic interactions with the Asp134, Ala135 and Gln157 residues. The π-π interaction appears to play a critical role in stabilizing the association of SAM with fibrillarin. Furthermore, comparison of A. pernix fibrillarin with homologous structures revealed different orientations of Phe110 and changes in α-helix 6 of fibrillarin and suggests key differences in its interactions with the adenine ring of SAM in the active site and with the C/D RNA. These differences may play a key role in orienting the SAM ligand for catalysis as well as in the assembly of other ribonucleoproteins and in the interactions with C/D RNA.

  18. Structure and magnetism in Fe-Gd based dinuclear and chain systems. The interplay of weak exchange coupling and zero field splitting effects.

    Science.gov (United States)

    Ferbinteanu, Marilena; Cimpoesu, Fanica; Gîrţu, Mihai A; Enachescu, Cristian; Tanase, Stefania

    2012-01-02

    The synthesis and characterization of two Fe-Gd systems based on bpca(-) (Hbpca = bis(2-pyridilcarbonyl)amine) as bridging ligand is presented, taking the systems as a case study for structure-property correlations. Compound 1, [Fe(LS)(II)(μ-bpca)(2)Gd(NO(3))(2)(H(2)O)]NO(3)·2CH(3)NO(2), is a zigzag polymer, incorporating the diamagnetic low spin Fe(LS)(II) ion. The magnetism of 1 is entirely determined by the weak zero field splitting (ZFS) effect on the Gd(III) ion. Compound 2 is a Fe(III)-Gd(III) dinuclear compound, [Fe(LS)(III)(bpca)(μ-bpca)Gd(NO(3))(4)]·4CH(3)NO(2)·CH(3)OH, its magnetism being interpreted as due to the antiferromagnetic coupling between the S(Fe) = ½ and S(Gd) = 7/2 spins, interplayed with the local ZFS on the lanthanide center. In both systems, the d-f assembly is determined by the bridging capabilities of the ambidentate bpca(-) ligand, which binds the d ion by a tridentate moiety with nitrogen donors and the f center by the diketonate side. We propose a spin delocalization and polarization mechanism that rationalizes the factors leading to the antiferromagnetic d-f coupling. Although conceived for compound 2, the scheme can be proposed as a general mechanism. The rationalization of the weak ZFS effects on Gd(III) by multiconfiguration and spin-orbit ab initio calculations allowed us to determine the details of the small but still significant anisotropy of Gd(III) ion in the coordination sites of compounds 1 and 2. The outlined methodologies and generalized conclusions shed new light on the field of gadolinium coordination magnetochemistry.

  19. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

    Energy Technology Data Exchange (ETDEWEB)

    Pletnev, Vladimir Z., E-mail: vzpletnev@gmail.com; Pletneva, Nadya V.; Lukyanov, Konstantin A.; Souslova, Ekaterina A.; Fradkov, Arkady F.; Chudakov, Dmitry M.; Chepurnykh, Tatyana; Yampolsky, Ilia V. [Russian Academy of Sciences, Moscow (Russian Federation); Wlodawer, Alexander [National Cancer Institute, Frederick, MD 21702 (United States); Dauter, Zbigniew [National Cancer Institute, Argonne, IL 60439 (United States); Pletnev, Sergei, E-mail: vzpletnev@gmail.com [National Cancer Institute, Argonne, IL 60439 (United States); SAIC-Frederick, Argonne, IL 60439 (United States); Russian Academy of Sciences, Moscow (Russian Federation)

    2013-09-01

    The crystal structure of the novel red emitting fluorescent protein from lancelet Branchiostoma lanceolatum (Chordata) revealed an unusual five residues cyclic unit comprising Gly58-Tyr59-Gly60 chromophore, the following Phe61 and Tyr62 covalently bound to chromophore Tyr59. A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the ‘core’ structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λ{sub ex}/λ{sub em} = 502/511 nm) and red laRFP (λ{sub ex}/λ{sub em} ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C{sup β} atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (

  20. Cosmology and the weak interaction

    Energy Technology Data Exchange (ETDEWEB)

    Schramm, D.N. (Fermi National Accelerator Lab., Batavia, IL (USA)):(Chicago Univ., IL (USA))

    1989-12-01

    The weak interaction plays a critical role in modern Big Bang cosmology. This review will emphasize two of its most publicized cosmological connections: Big Bang nucleosynthesis and Dark Matter. The first of these is connected to the cosmological prediction of Neutrino Flavours, N{sub {nu}} {approximately} 3 which is now being confirmed at SLC and LEP. The second is interrelated to the whole problem of galaxy and structure formation in the universe. This review will demonstrate the role of the weak interaction both for dark matter candidates and for the problem of generating seeds to form structure. 87 refs., 3 figs., 5 tabs.

  1. Structural basis for the oxidation of protein-bound sulfur by the sulfur cycle molybdohemo-enzyme sulfane dehydrogenase SoxCD.

    Science.gov (United States)

    Zander, Ulrich; Faust, Annette; Klink, Björn U; de Sanctis, Daniele; Panjikar, Santosh; Quentmeier, Armin; Bardischewsky, Frank; Friedrich, Cornelius G; Scheidig, Axel J

    2011-03-11

    The sulfur cycle enzyme sulfane dehydrogenase SoxCD is an essential component of the sulfur oxidation (Sox) enzyme system of Paracoccus pantotrophus. SoxCD catalyzes a six-electron oxidation reaction within the Sox cycle. SoxCD is an α(2)β(2) heterotetrameric complex of the molybdenum cofactor-containing SoxC protein and the diheme c-type cytochrome SoxD with the heme domains D(1) and D(2). SoxCD(1) misses the heme-2 domain D(2) and is catalytically as active as SoxCD. The crystal structure of SoxCD(1) was solved at 1.33 Å. The substrate of SoxCD is the outer (sulfane) sulfur of Cys-110-persulfide located at the C-terminal peptide swinging arm of SoxY of the SoxYZ carrier complex. The SoxCD(1) substrate funnel toward the molybdopterin is narrow and partially shielded by side-chain residues of SoxD(1). For access of the sulfane-sulfur of SoxY-Cys-110 persulfide we propose that (i) the blockage by SoxD-Arg-98 is opened via interaction with the C terminus of SoxY and (ii) the C-terminal peptide VTIGGCGG of SoxY provides interactions with the entrance path such that the cysteine-bound persulfide is optimally positioned near the molybdenum atom. The subsequent oxidation reactions of the sulfane-sulfur are initiated by the nucleophilic attack of the persulfide anion on the molybdenum atom that is, in turn, reduced. The close proximity of heme-1 to the molybdopterin allows easy acceptance of the electrons. Because SoxYZ, SoxXA, and SoxB are already structurally characterized, with SoxCD(1) the structures of all key enzymes of the Sox cycle are known with atomic resolution.

  2. Crystal structure of calpain-3 penta-EF-hand (PEF) domain - a homodimerized PEF family member with calcium bound at the fifth EF-hand.

    Science.gov (United States)

    Partha, Sarathy K; Ravulapalli, Ravikiran; Allingham, John S; Campbell, Robert L; Davies, Peter L

    2014-07-01

    Calpains are Ca(2+) dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca(2+) signaling in the cell. The major isoforms of this enzyme family, calpain-1 and calpain-2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C-terminal penta-EF hand (PEF) domains. Calpain-3, or p94, is a skeletal muscle-specific isoform that is genetically linked to limb-girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain-3 support the suggestion that full-length calpain-3 exists as a homodimer. Here, we report the crystallization of calpain-3's PEF domain and its crystal structure in the presence of Ca(2+) , which provides evidence for the homodimer architecture of calpain-3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain-3 PEF domain contains a Ca(2+) bound at the EF5-hand used for homodimer association. Three of the four Ca(2+) -binding EF-hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca(2+) signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain-3 large subunit were to try to pair with a calpain small subunit. Database Structural data are available in the Protein Data Bank database under accession number 4OKH. © 2014 FEBS.

  3. Structure of the Human Angiotensin II Type 1 (AT1) Receptor Bound to Angiotensin II from Multiple Chemoselective Photoprobe Contacts Reveals a Unique Peptide Binding Mode*

    Science.gov (United States)

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-01-01

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs. PMID:23386604

  4. Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Junya [Division of Biological Science, Graduate School of Science, Nagoya University (Japan); Hirano, Hidemi [Division of Biological Science, Graduate School of Science, Nagoya University (Japan); Structural Biology Research Center, Graduate School of Science, Nagoya University (Japan); Matsuura, Yoshiyuki, E-mail: matsuura.yoshiyuki@d.mbox.nagoya-u.ac.jp [Division of Biological Science, Graduate School of Science, Nagoya University (Japan); Structural Biology Research Center, Graduate School of Science, Nagoya University (Japan)

    2015-07-31

    In Saccharomyces cerevisiae, the protein phosphatase Cdc14p is an antagonist of mitotic cyclin-dependent kinases and is a key regulator of late mitotic events such as chromosome segregation, spindle disassembly and cytokinesis. The activity of Cdc14p is controlled by cell-cycle dependent changes in its association with its competitive inhibitor Net1p (also known as Cfi1p) in the nucleolus. For most of the cell cycle up to metaphase, Cdc14p is sequestered in the nucleolus in an inactive state. During anaphase, Cdc14p is released from Net1p, spreads into the nucleus and cytoplasm, and dephosphorylates key mitotic targets. Although regulated nucleocytoplasmic shuttling of Cdc14p has been suggested to be important for exit from mitosis, the mechanism underlying Cdc14p nuclear trafficking remains poorly understood. Here we show that the C-terminal region (residues 517–551) of Cdc14p can function as a nuclear localization signal (NLS) in vivo and also binds to Kap121p (also known as Pse1p), an essential nuclear import carrier in yeast, in a Gsp1p-GTP-dependent manner in vitro. Moreover we report a crystal structure, at 2.4 Å resolution, of Kap121p bound to the C-terminal region of Cdc14p. The structure and structure-based mutational analyses suggest that either the last five residues at the extreme C-terminus of Cdc14p (residues 547–551; Gly-Ser-Ile-Lys-Lys) or adjacent residues with similar sequence (residues 540–544; Gly-Gly-Ile-Arg-Lys) can bind to the NLS-binding site of Kap121p, with two residues (Ile in the middle and Lys at the end of the five residues) of Cdc14p making key contributions to the binding specificity. Based on comparison with other structures of Kap121p-ligand complexes, we propose “IK-NLS” as an appropriate term to refer to the Kap121p-specific NLS. - Highlights: • The C-terminus of Cdc14p binds to Kap121p in a Gsp1p-GTP-dependent manner. • The crystal structure of Kap121p-Cdc14p complex is determined. • The structure reveals how

  5. Structures of the substrate-free and product-bound forms of HmuO, a heme oxygenase from corynebacterium diphtheriae: x-ray crystallography and molecular dynamics investigation.

    Science.gov (United States)

    Unno, Masaki; Ardèvol, Albert; Rovira, Carme; Ikeda-Saito, Masao

    2013-11-29

    Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe(3+)-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe(3+)-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe(3+)-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe(3+)-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit.

  6. Structural and thermodynamic insight into the process of "weak" dimerization of the ErbB4 transmembrane domain by solution NMR.

    Science.gov (United States)

    Bocharov, Eduard V; Mineev, Konstantin S; Goncharuk, Marina V; Arseniev, Alexander S

    2012-09-01

    Specific helix-helix interactions between the single-span transmembrane domains of receptor tyrosine kinases are believed to be important for their lateral dimerization and signal transduction. Establishing structure-function relationships requires precise structural-dynamic information about this class of biologically significant bitopic membrane proteins. ErbB4 is a ubiquitously expressed member of the HER/ErbB family of growth factor receptor tyrosine kinases that is essential for the normal development of various adult and fetal human tissues and plays a role in the pathobiology of the organism. The dimerization of the ErbB4 transmembrane domain in membrane-mimicking lipid bicelles was investigated by solution NMR. In a bicellar DMPC/DHPC environment, the ErbB4 membrane-spanning α-helices (651-678)(2) form a right-handed parallel dimer through the N-terminal double GG4-like motif A(655)GxxGG(660) in a fashion that is believed to permit proper kinase domain activation. During helix association, the dimer subunits undergo a structural adjustment (slight bending) with the formation of a network of inter-monomeric polar contacts. The quantitative analysis of the observed monomer-dimer equilibrium provides insights into the kinetics and thermodynamics of the folding process of the helical transmembrane domain in the model environment that may be directly relevant to the process that occurs in biological membranes. The lipid bicelles occupied by a single ErbB4 transmembrane domain behave as a true ("ideal") solvent for the peptide, while multiply occupied bicelles are more similar to the ordered lipid microdomains of cellular membranes and appear to provide substantial entropic enhancement of the weak helix-helix interactions, which may be critical for membrane protein activity. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Rigorous coherent-structure theory for falling liquid films: Viscous dispersion effects on bound-state formation and self-organization

    CERN Document Server

    Pradas, Marc; Kalliadasis, Serafim

    2011-01-01

    We examine the interaction of two-dimensional solitary pulses on falling liquid films. We make use of the second-order model derived by Ruyer-Quil and Manneville [Eur. Phys. J. B 6, 277 (1998); Eur. Phys. J. B 15, 357 (2000); Phys. Fluids 14, 170 (2002)] by combining the long-wave approximation with a weighted residuals technique. The model includes (second-order) viscous dispersion effects which originate from the streamwise momentum equation and tangential stress balance. These effects play a dispersive role that primarily influences the shape of the capillary ripples in front of the solitary pulses. We show that different physical parameters, such as surface tension and viscosity, play a crucial role in the interaction between solitary pulses giving rise eventually to the formation of bound states consisting of two or more pulses separated by well-defined distances and travelling at the same velocity. By developing a rigorous coherent-structure theory, we are able to theoretically predict the pulse-separat...

  8. X-ray structures of the proprotein convertase furin bound with substrate analog inhibitors reveal substrate specificity determinants beyond the S4 pocket.

    Science.gov (United States)

    Dahms, Sven O; Hardes, Kornelia; Steinmetzer, Torsten; Than, Manuel E

    2018-01-09

    The proprotein convertase (PC) furin is a highly specific serine protease modifying and thereby activating proteins in the secretory pathway by proteolytic cleavage. Its substrates are involved in many diseases including cancer and infections caused by bacteria and viruses. Understanding furin's substrate specificity is of crucial importance for the development of pharmacologically applicable inhibitors. Using protein X-ray crystallography we investigated the extended substrate binding site of furin in complex with three peptide derived inhibitors at up to 1.9 Å resolution. The structure of the protease bound with a hexapeptide inhibitor revealed molecular details of its S6 pocket, which remained completely unknown so far. The arginine residue at P6 induced an unexpected turn-like conformation of the inhibitor backbone, which is stabilized by intra- and intermolecular H-bonds. In addition, we confirmed the binding of arginine to the previously proposed S5 pocket (S51). An alternative S5 site (S52) could be utilized by shorter sidechains as demonstrated for a 4-aminomethyl-phenylacetyl residue, which shows steric properties similar to a lysine side chain. Interestingly, we also observed binding of a peptide with citrulline at P4 substituting the highly conserved arginine. The structural data might indicate an unusual protonation state of Asp264 maintaining the interaction with uncharged citrulline. The herein identified molecular interaction sites at P5 and P6 can be utilized to improve next generation furin inhibitors. Our data will also help to predict furin substrates more precisely based on the additional specificity determinants observed for P5 and P6.

  9. Crystal structure of calpain-3 penta-EF-hand (PEF) domain - a homodimerized PEF family member with calcium bound at the fifth EF-hand

    Energy Technology Data Exchange (ETDEWEB)

    Partha, Sarathy K.; Ravulapalli, Ravikiran; Allingham, John S.; Campbell, Robert L.; Davies, Peter L. [Queens

    2014-08-21

    Calpains are Ca2+dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca2+ signaling in the cell. The major isoforms of this enzyme family, calpain-1 and calpain-2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C-terminal penta-EF hand (PEF) domains. Calpain-3, or p94, is a skeletal muscle-specific isoform that is genetically linked to limb-girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain-3 support the suggestion that full-length calpain-3 exists as a homodimer. Here, we report the crystallization of calpain-3's PEF domain and its crystal structure in the presence of Ca2+, which provides evidence for the homodimer architecture of calpain-3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain-3 PEF domain contains a Ca2+ bound at the EF5-hand used for homodimer association. Three of the four Ca2+-binding EF-hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca2+ signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain-3 large subunit were to try to pair with a calpain small subunit.

  10. The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4). X-ray crystal structure of the complex and molecular dynamics characterization of the binding site.

    Science.gov (United States)

    Tempel, Wolfram; Tschampel, Sarah; Woods, Robert J

    2002-02-22

    The shortage of organs for transplantation into human patients continues to be a driving force behind research into the use of tissues from non-human donors, particularly pig. The primary barrier to such xenotransplantation is the reaction between natural antibodies present in humans and Old World monkeys and the Gal alpha(1-3)Gal epitope (xenograft antigen, xenoantigen) found on the cell surfaces of the donor organ. This hyperacute immune response leads ultimately to graft rejection. Because of its high specificity for the xenograft antigen, isolectin 1-B(4) from Griffonia simplicifolia (GS-1-B(4)) has been used as an immunodiagnostic reagent. Furthermore, haptens that inhibit natural antibodies also inhibit GS-1-B(4) from binding to the xenoantigen. Here we report the first x-ray crystal structure of the xenograft antigen bound to a protein (GS-1-B(4)). The three-dimensional structure was determined from orthorhombic crystals at a resolution of 2.3 A. To probe the influence of binding on ligand properties, we report also the results of molecular dynamics (MD) simulations on this complex as well as on the free ligand. The MD simulations were performed with the AMBER force-field for proteins augmented with the GLYCAM parameters for glycosides and glycoproteins. The simulations were performed for up to 10 ns in the presence of explicit solvent. Through comparison with MD simulations performed for the free ligand, it has been determined that GS-1-B(4) recognizes the lowest energy conformation of the disaccharide. In addition, the x-ray and modeling data provide clear explanations for the reported specificities of the GS-1-B(4) lectin. It is anticipated that a further understanding of the interactions involving the xenograft antigen will help in the development of therapeutic agents for application in the prevention of hyperacute xenograft rejection.

  11. Corrugation in the Weakly Interacting Hexagonal-BN/Cu(111) System: Structure Determination by Combining Noncontact Atomic Force Microscopy and X-ray Standing Waves.

    Science.gov (United States)

    Schwarz, Martin; Riss, Alexander; Garnica, Manuela; Ducke, Jacob; Deimel, Peter S; Duncan, David A; Thakur, Pardeep Kumar; Lee, Tien-Lin; Seitsonen, Ari Paavo; Barth, Johannes V; Allegretti, Francesco; Auwärter, Willi

    2017-09-26

    Atomically thin hexagonal boron nitride (h-BN) layers on metallic supports represent a promising platform for the selective adsorption of atoms, clusters, and molecular nanostructures. Specifically, scanning tunneling microscopy (STM) studies revealed an electronic corrugation of h-BN/Cu(111), guiding the self-assembly of molecules and their energy level alignment. A detailed characterization of the h-BN/Cu(111) interface including the spacing between the h-BN sheet and its support-elusive to STM measurements-is crucial to rationalize the interfacial interactions within these systems. To this end, we employ complementary techniques including high-resolution noncontact atomic force microscopy, STM, low-energy electron diffraction, X-ray photoelectron spectroscopy, the X-ray standing wave method, and density functional theory. Our multimethod study yields a comprehensive, quantitative structure determination including the adsorption height and the corrugation of the sp(2) bonded h-BN layer on Cu(111). Based on the atomic contrast in atomic force microscopy measurements, we derive a measurable-hitherto unrecognized-geometric corrugation of the h-BN monolayer. This experimental approach allows us to spatially resolve minute height variations in low-dimensional nanostructures, thus providing a benchmark for theoretical modeling. Regarding potential applications, e.g., as a template or catalytically active support, the recognition of h-BN on Cu(111) as a weakly bonded and moderately corrugated overlayer is highly relevant.

  12. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-03-19

    This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.

  13. Space group constraints on weak indices in topological insulators

    NARCIS (Netherlands)

    Varjas, D.; De Juan, Fernando; Lu, Yuan Ming

    Lattice translation symmetry gives rise to a large class of "weak" topological insulators (TIs), characterized by translation-protected gapless surface states and dislocation bound states. In this work we show that space group symmetries lead to constraints on the weak topological indices that

  14. Crystal structure of monoclinic samarium and cubic europium sesquioxides and bound coherent neutron scattering lengths of the isotopes {sup 154}Sm and {sup 153}Eu

    Energy Technology Data Exchange (ETDEWEB)

    Kohlmann, Holger [Leipzig Univ. (Germany). Inst. of Inorganic Chemistry; Hein, Christina; Kautenburger, Ralf [Saarland Univ., Saarbruecken (Germany). Inorganic Solid State Chemistry; Hansen, Thomas C.; Ritter, Clemens [Institut Laue-Langevin, Grenoble (France); Doyle, Stephen [Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany). Inst. for Synchrotron Radiation (ISS)

    2016-11-01

    The crystal structures of monoclinic samarium and cubic europium sesquioxide, Sm{sub 2}O{sub 3} and Eu{sub 2}O{sub 3}, were reinvestigated by powder diffraction methods (laboratory X-ray, synchrotron, neutron). Rietveld analysis yields more precise structural parameters than previously known, especially for oxygen atoms. Interatomic distances d(Sm-O) in Sm{sub 2}O{sub 3} range from 226.3(4) to 275.9(2) pm [average 241.6(3) pm] for the monoclinic B type Sm{sub 2}O{sub 3} [space group C2/m, a = 1418.04(3) pm, b = 362.660(7) pm, c = 885.48(2) pm, β = 100.028(1) ], d(Eu-O) in Eu{sub 2}O{sub 3} from 229.9(2) to 238.8(2) pm for the cubic bixbyite (C) type [space group Ia anti 3, a = 1086.87(1) pm]. Neutron diffraction at 50 K and 2 K did not show any sign for magnetic ordering in Sm{sub 2}O{sub 3}. Isotopically enriched {sup 154}Sm{sub 2}O{sub 3} and {sup 153}Eu{sub 2}O{sub 3} were used for the neutron diffraction work because of the enormous absorption cross section of the natural isotopic mixtures for thermal neutrons. The isotopic purity was determined by inductively coupled plasma - mass spectrometry to be 98.9% for {sup 154}Sm and 99.8% for {sup 153}Eu. Advanced analysis of the neutron diffraction data suggest that the bound coherent scattering lengths of {sup 154}Sm and {sup 153}Eu need to be revised. We tentatively propose b{sub c}({sup 154}Sm) = 8.97(6) fm and b{sub c}({sup 153}Eu) = 8.85(3) fm for a neutron wavelength of 186.6 pm to be better values for these isotopes, showing up to 8% deviation from accepted literature values. It is shown that inaccurate scattering lengths may result in severe problems in crystal structure refinements causing erroneous structural details such as occupation parameters, which might be critically linked to physical properties like superconductivity in multinary oxides.

  15. Bounding solutions for cerebral aneurysms

    NARCIS (Netherlands)

    Mikhal, Julia Olegivna; Geurts, Bernardus J.

    2011-01-01

    Cerebral aneurysms are weak spots in the vessel structure of the brain, which present a serious problem to the patient. Julia Mikhal and Bernard Geurts present the application of an Immersed Boundary (IB) method to the simulation of blood flow through such aneurysms. The goal is to understand the

  16. Coexistence of Weak Ferromagnetism and Polar Lattice Distortion in Epitaxial NiTiO3 thin films of the LiNbO3-Type Structure

    Energy Technology Data Exchange (ETDEWEB)

    Varga, Tamas [Environmental Molecular Sciences Lab., Richland, WA (United States); Droubay, Timothy C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bowden, Mark E. [Environmental Molecular Sciences Lab., Richland, WA (United States); Colby, Robert J. [Environmental Molecular Sciences Lab., Richland, WA (United States); Manandhar, Sandeep [Environmental Molecular Sciences Lab., Richland, WA (United States); Shutthanandan, Vaithiyalingam [Environmental Molecular Sciences Lab., Richland, WA (United States); Hu, Dehong [Environmental Molecular Sciences Lab., Richland, WA (United States); Kabius, Bernd C. [Environmental Molecular Sciences Lab., Richland, WA (United States); Apra, Edoardo [Environmental Molecular Sciences Lab., Richland, WA (United States); Shelton, William A. [Environmental Molecular Sciences Lab., Richland, WA (United States); Chambers, Scott A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-04-15

    We report the magnetic and structural characteristics of epitaxial NiTiO3 films grown by pulsed laser deposition that are isostructural with acentric LiNbO3 (space group R3c). Optical second harmonic generation and magnetometry demonstrate lattice polarization at room temperature and weak ferromagnetism below 250 K, respectively. These results appear to be consistent with earlier predictions from first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LiNbO3 structure. This acentric form of NiTiO3 is believed to be one of the rare examples of ferroelectrics exhibiting weak ferromagnetism generated by a Dzyaloshinskii-Moriya interaction.

  17. Anomalously Weak Solar Convection

    Science.gov (United States)

    Hanasoge, Shravan M.; Duvall, Thomas L.; Sreenivasan, Katepalli R.

    2012-01-01

    Convection in the solar interior is thought to comprise structures on a spectrum of scales. This conclusion emerges from phenomenological studies and numerical simulations, though neither covers the proper range of dynamical parameters of solar convection. Here, we analyze observations of the wavefield in the solar photosphere using techniques of time-distance helioseismology to image flows in the solar interior. We downsample and synthesize 900 billion wavefield observations to produce 3 billion cross-correlations, which we average and fit, measuring 5 million wave travel times. Using these travel times, we deduce the underlying flow systems and study their statistics to bound convective velocity magnitudes in the solar interior, as a function of depth and spherical- harmonic degree l..Within the wavenumber band l convective velocities are 20-100 times weaker than current theoretical estimates. This constraint suggests the prevalence of a different paradigm of turbulence from that predicted by existing models, prompting the question: what mechanism transports the heat flux of a solar luminosity outwards? Advection is dominated by Coriolis forces for wavenumbers l convection may be quasi-geostrophic. The fact that isorotation contours in the Sun are not coaligned with the axis of rotation suggests the presence of a latitudinal entropy gradient.

  18. Bounded Parikh Automata

    Directory of Open Access Journals (Sweden)

    Michaël Cadilhac

    2011-08-01

    Full Text Available The Parikh finite word automaton model (PA was introduced and studied by Klaedtke and Ruess in 2003. Here, by means of related models, it is shown that the bounded languages recognized by PA are the same as those recognized by deterministic PA. Moreover, this class of languages is the class of bounded languages whose set of iterations is semilinear.

  19. Bounded Gaussian process regression

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Nielsen, Jens Brehm; Larsen, Jan

    2013-01-01

    We extend the Gaussian process (GP) framework for bounded regression by introducing two bounded likelihood functions that model the noise on the dependent variable explicitly. This is fundamentally different from the implicit noise assumption in the previously suggested warped GP framework. We...

  20. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  1. Synthesis, crystal structure, weak antiferromagnetic behavior and electronic studies of novel [((-)-sparteine)(PhCO 2)(Cl)]Cu(II) complex

    Science.gov (United States)

    Alcántara-Flores, José Luis; Vázquez-Bravo, José Jaime; Gutiérrez-Pérez, René; Ramírez-Rosales, Daniel; Bernès, Sylvain; Ramírez Bokhimi, José Guadalupe; Zamorano-Ulloa, Rafael; Reyes-Ortega, Yasmi

    2003-09-01

    [((-)-Sparteine)(PhCO 2)(Cl)]Cu(II) 1 complex is obtained by direct synthesis using copper(0). 1 crystallizes in the monoclinic space group P2 1 with a=14.7355(12), b=8.9768(5), c=17.2810(10) Å, β=111.916(5)°, and Z=4. The electronic spectrum of 1 shows a broad band with λ max˜841 nm(ɛ=0.261 mM-1 cm-6) characteristic of a low symmetry and tetragonally distorted square pyramidal local Cu geometry. The far IR spectrum of 1 shows characteristic vibrations of Cu-Cl (260, 267 cm -1), Cu-N (436, 467 cm -1) and Cu-O (457 cm -1) bonds. The 1H NMR spectrum of 1 is typical of magnetic Cu(II) complexes with line broadening due to efficient nuclear relaxation from the metal center. ESR spectra of polycrystalline 1 at 77 K show an axial spectrum with linewidth of 58.6 G and at 300 K of 89.0 G, with areas in the ratio A77/ A300=2.79, indicative of antiferromagnetic order. The linewidth is reduced by 34% on going from 300 to 77 K. Standard magnetization measurements at low temperatures show an Curie-Weiss behavior with θ=-21.67 K, suggesting a weak exchange coupling interaction. The crystalline structure of 1 shows that the lattice is arranged so that the space between molecules is smaller than 40 Å 3, not enough to accommodate solvent molecules. However, the shortest Cu-Cu contact is 7.5912(8) Å.

  2. Gossip and Distributed Kalman Filtering: Weak Consensus Under Weak Detectability

    Science.gov (United States)

    Kar, Soummya; Moura, José M. F.

    2011-04-01

    The paper presents the gossip interactive Kalman filter (GIKF) for distributed Kalman filtering for networked systems and sensor networks, where inter-sensor communication and observations occur at the same time-scale. The communication among sensors is random; each sensor occasionally exchanges its filtering state information with a neighbor depending on the availability of the appropriate network link. We show that under a weak distributed detectability condition: 1. the GIKF error process remains stochastically bounded, irrespective of the instability properties of the random process dynamics; and 2. the network achieves \\emph{weak consensus}, i.e., the conditional estimation error covariance at a (uniformly) randomly selected sensor converges in distribution to a unique invariant measure on the space of positive semi-definite matrices (independent of the initial state.) To prove these results, we interpret the filtered states (estimates and error covariances) at each node in the GIKF as stochastic particles with local interactions. We analyze the asymptotic properties of the error process by studying as a random dynamical system the associated switched (random) Riccati equation, the switching being dictated by a non-stationary Markov chain on the network graph.

  3. Multipole-bound molecular negative ions

    CERN Document Server

    Abdul-Karim, H; Desfrançois, C

    2002-01-01

    Within the framework of a simple electrostatic model, as compared to recent experimental results, we here discuss the stability of very weakly bound molecular negative ions. In contrast with the case of conventional valence anions, the excess electron is then located in a very diffuse orbital and is mainly bound by electrostatic dipolar, quadrupolar, and polarization forces, at large distances from the neutral molecular core. By fitting a single repulsion parameter of the model to the available experimental data, it is possible to make quantitative predictions of the excess-electron binding energies in these species. Critical values of the dipole moment, quadrupole moment or polarizability required for the observation of stable multipole-bound negative ions are predicted and compared to available experimental data and ab initio calculations. Refs. 26 (author)

  4. On the molecular basis of the recognition of angiotensin II (AII). NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131.

    Science.gov (United States)

    Tzakos, Andreas G; Bonvin, Alexandre M J J; Troganis, Anasstasios; Cordopatis, Paul; Amzel, Mario L; Gerothanassis, Ioannis P; van Nuland, Nico A J

    2003-03-01

    The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints. After final refinement in explicit water, a family of 13 structures was obtained with a backbone RMSD of 0.73 +/- 0.23 A. AII adopts a fairly compact folded structure, with its C-terminus and N-terminus approaching to within approximately 7.2 A of each other. The side chains of Arg2, Tyr4, Ile5 and His6 are oriented on one side of a plane defined by the peptide backbone, and the Val3 and Pro7 are pointing in opposite directions. The stabilization of the folded conformation can be explained by the stacking of the Val3 side chain with the Pro7 ring and by a hydrophobic cluster formed by the Tyr4, Ile5 and His6 side chains. Comparison between the NMR-derived structure of AII in aqueous solution and the refined crystal structure of the complex of AII with a high-affinity mAb (Fab131) [Garcia, K.C., Ronco, P.M., Verroust, P.J., Brunger, A.T., Amzel, L.M. (1992) Science257, 502-507] provides important quantitative information on two common structural features: (a) a U-shaped structure of the Tyr4-Ile5-His6-Pro7 sequence, which is the most immunogenic epitope of the peptide, with the Asp1 side chain oriented towards the interior of the turn approaching the C-terminus; (b) an Asx-turn-like motif with the side chain aspartate carboxyl group hydrogen-bonded to the main chain NH group of Arg2. It can be concluded that small rearrangements of the epitope 4-7 in the solution structure of AII are required by a mean value of 0.76 +/- 0.03 A for structure alignment and approximately 1.27 +/- 0.02 A for sequence alignment with the X-ray structure of AII bound to the mAb Fab131. These data are interpreted in terms of a biological "nucleus" conformation of the hormone in solution, which requires a limited number of structural rearrangements for receptor-antigen recognition and binding.

  5. Strengths and weaknesses of Global Positioning System (GPS) data-loggers and semi-structured interviews for capturing fine-scale human mobility: findings from Iquitos, Peru.

    Science.gov (United States)

    Paz-Soldan, Valerie A; Reiner, Robert C; Morrison, Amy C; Stoddard, Steven T; Kitron, Uriel; Scott, Thomas W; Elder, John P; Halsey, Eric S; Kochel, Tadeusz J; Astete, Helvio; Vazquez-Prokopec, Gonzalo M

    2014-06-01

    Quantifying human mobility has significant consequences for studying physical activity, exposure to pathogens, and generating more realistic infectious disease models. Location-aware technologies such as Global Positioning System (GPS)-enabled devices are used increasingly as a gold standard for mobility research. The main goal of this observational study was to compare and contrast the information obtained through GPS and semi-structured interviews (SSI) to assess issues affecting data quality and, ultimately, our ability to measure fine-scale human mobility. A total of 160 individuals, ages 7 to 74, from Iquitos, Peru, were tracked using GPS data-loggers for 14 days and later interviewed using the SSI about places they visited while tracked. A total of 2,047 and 886 places were reported in the SSI and identified by GPS, respectively. Differences in the concordance between methods occurred by location type, distance threshold (within a given radius to be considered a match) selected, GPS data collection frequency (i.e., 30, 90 or 150 seconds) and number of GPS points near the SSI place considered to define a match. Both methods had perfect concordance identifying each participant's house, followed by 80-100% concordance for identifying schools and lodgings, and 50-80% concordance for residences and commercial and religious locations. As the distance threshold selected increased, the concordance between SSI and raw GPS data increased (beyond 20 meters most locations reached their maximum concordance). Processing raw GPS data using a signal-clustering algorithm decreased overall concordance to 14.3%. The most common causes of discordance as described by a sub-sample (n=101) with whom we followed-up were GPS units being accidentally off (30%), forgetting or purposely not taking the units when leaving home (24.8%), possible barriers to the signal (4.7%) and leaving units home to recharge (4.6%). We provide a quantitative assessment of the strengths and weaknesses of

  6. WEAK GORENSTEIN GLOBAL DIMENSION

    OpenAIRE

    Bennis, Driss

    2010-01-01

    In this paper, we investigate the weak Gorenstein global dimensions. We are mainly interested in studying the problem when the left and right weak Gorenstein global dimensions coincide. We first show, for GF-closed rings, that the left and right weak Gorenstein global dimensions are equal when they are finite. Then, we prove that the same equality holds for any two-sided coherent ring. We conclude the paper with some examples and a brief discussion of the scope and limits of our results.

  7. Virial Expansion Bounds

    Science.gov (United States)

    Tate, Stephen James

    2013-10-01

    In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.

  8. History of Weak Interactions

    Science.gov (United States)

    Lee, T. D.

    1970-07-01

    While the phenomenon of beta-decay was discovered near the end of the last century, the notion that the weak interaction forms a separate field of physical forces evolved rather gradually. This became clear only after the experimental discoveries of other weak reactions such as muon-decay, muon-capture, etc., and the theoretical observation that all these reactions can be described by approximately the same coupling constant, thus giving rise to the notion of a universal weak interaction. Only then did one slowly recognize that the weak interaction force forms an independent field, perhaps on the same footing as the gravitational force, the electromagnetic force, and the strong nuclear and sub-nuclear forces.

  9. Crystal structure of a class-mu glutathione S-transferase from whiteleg shrimp Litopenaeus vannamei: structural changes in the xenobiotic binding H-site may alter the spectra of molecules bound.

    Science.gov (United States)

    Juárez-Martínez, Ariadna B; Sotelo-Mundo, Rogerio R; Rudiño-Piñera, Enrique

    2017-02-01

    Glutathione S-transferases (GSTs) are dimeric proteins that play a key role in phase II cellular detoxification. Here, the first crystal structure of a GST class-mu from marine crustacean shrimp Litopenaeus vannamei is reported at a resolution of 2.0 Å. The coordinates reported here have the lowest sequence identity with previously reported GSTs class-mu deposited at the Protein Data Bank (PDB), although they have subtle conformational differences. One key feature of GST class-mu from L. vannamei is the active site crevice markedly reduced when it is compared with other GSTs class-mu. This finding together with the chemical change of residues into the cavity (F112 and Y210) points to a particular specialization in which smallest xenobiotics with nonstandard chemical characteristics can be bound to the H-site. This suggests that marine organisms have evolved structural strategies to provide efficient selectivity toward xenobiotics to be disposed of by the phase II detoxification process. © 2016 Wiley Periodicals, Inc.

  10. Non-perturbative aspects in a weakly interacting Higgs sector

    CERN Document Server

    Maas, Axel

    2012-01-01

    Just like the weakly interacting QED can support non-perturbative phenomena, like atoms, so can the weak and Higgs interactions. Especially, there are strong field-theoretical arguments that only bound states can be the (quasi-)asymptotic physical degrees of freedom of this sector. After a brief review of these arguments, the 2-point, 3-point and 4-point correlation functions of the Higgs-W system are determined using lattice gauge theory. The results support a conjectured duality between elementary states and bound states for weak Higgs self-interactions. This leads to relations between the bound states and the experimentally observed particles. Interestingly, these may yield pseudo-scalar admixtures at the Higgs energy, and possibly a faint standard-model signal in the channel where a Kaluza-Klein graviton would be expected.

  11. Validation of EMP bounds

    Energy Technology Data Exchange (ETDEWEB)

    Warne, L.K.; Merewether, K.O.; Chen, K.C.; Jorgenson, R.E.; Morris, M.E.; Solberg, J.E.; Lewis, J.G. [Sandia National Labs., Albuquerque, NM (United States); Derr, W. [Derr Enterprises, Albuquerque, NM (United States)

    1996-07-01

    Test data on canonical weapon-like fixtures are used to validate previously developed analytical bounding results. The test fixtures were constructed to simulate (but be slightly worse than) weapon ports of entry but have known geometries (and electrical points of contact). The exterior of the test fixtures exhibited exterior resonant enhancement of the incident fields at the ports of entry with magnitudes equal to those of weapon geometries. The interior consisted of loaded transmission lines adjusted to maximize received energy or voltage but incorporating practical weapon geometrical constraints. New analytical results are also presented for bounding the energies associated with multiple bolt joints and for bounding the exterior resonant enhancement of the exciting fields.

  12. Acyldepsipeptide Antibiotics Induces the Formation of a Structured Axial Channel in ClpP: a Model for the ClpX/ClpA Bound State of ClpP

    OpenAIRE

    Li, Dominic Him Shun; Chung, Yu Seon; Gloyd, Melanie; Joseph, Ebenezer; Ghirlando, Rodolfo; Wright, Gerard D.; Cheng, Yi-Qiang; Maurizi, Michael R.; Guarné, Alba; Ortega, Joaquin

    2010-01-01

    In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli ClpP bound to ADEP1 and report the structural changes underlying ClpP activation. ADEP1 binds in the h...

  13. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Faust, Sebastian; Mukherjee, Pratyay

    2013-01-01

    a bounded tamper and leakage resilient CCA secure public key cryptosystem based on the DDH assumption. We first define a weaker CPA-like security notion that we can instantiate based on DDH, and then we give a general compiler that yields CCA-security with tamper and leakage resilience. This requires...... a public tamper-proof common reference string. Finally, we explain how to boost bounded tampering and leakage resilience (as in 1. and 2. above) to continuous tampering and leakage resilience, in the so-called floppy model where each user has a personal hardware token (containing leak- and tamper...

  14. Structure of Amantadine-Bound M2 Transmembrane Peptide of Influenza A in Lipid Bilayers from Magic-Angle-Spinning Solid-State NMR: the Role of Ser31 in Amantadine Binding

    Science.gov (United States)

    Cady, Sarah D.; Mishanina, Tatiana V.; Hong, Mei

    2014-01-01

    The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine, whose effectiveness has been abolished by a single-site mutation of Ser31 to Asn in the transmembrane domain of the protein. Recent high-resolution structures of the M2 transmembrane domain obtained from detergent-solubilized protein in solution and crystal environments gave conflicting drug binding sites. We present magic-angle-spinning solid-state NMR results of Ser31 and a number of other residues in the M2 transmembrane peptide (M2TMP) bound to lipid bilayers. Comparison of the spectra of the membrane-bound apo and complexed M2TMP indicates that Ser31 is the site of the largest chemical shift perturbation by amantadine. The chemical shift constraints lead to a monomer structure with a small kink of the helical axis at Gly34. A tetramer model is then constructed using the helix tilt angle and several interhelical distances previously measured on unoriented bilayer samples. This tetramer model differs from the solution and crystal structures in terms of the openness of the N-terminus of the channel, the constriction at Ser31, and the sidechain conformations of Trp41, a residue important for channel gating. Moreover, the tetramer model suggests that Ser31 may interact with amantadine amine via hydrogen bonding. While the apo and drug-bound M2TMP have similar average structures, the complexed peptide has much narrower linewidths at physiological temperature, indicating drug-induced changes of the protein dynamics in the membrane. Further, at low temperature, several residues show narrower lines in the complexed peptide than the apo peptide, indicating that amantadine binding reduces the conformational heterogeneity of specific residues. The differences of the current solid-state NMR structure of the bilayer-bound M2TMP from the detergent-based M2 structures suggest that the M2 conformation is sensitive to the environment, and care must be taken when interpreting

  15. Bagging Weak Predictors

    DEFF Research Database (Denmark)

    Lukas, Manuel; Hillebrand, Eric

    Relations between economic variables can often not be exploited for forecasting, suggesting that predictors are weak in the sense that estimation uncertainty is larger than bias from ignoring the relation. In this paper, we propose a novel bagging predictor designed for such weak predictor...... variables. The predictor is based on a test for finitesample predictive ability. Our predictor shrinks the OLS estimate not to zero, but towards the null of the test which equates squared bias with estimation variance. We derive the asymptotic distribution and show that the predictor can substantially lower...

  16. Weak gravity conjecture and effective field theory

    Science.gov (United States)

    Saraswat, Prashant

    2017-01-01

    The weak gravity conjecture (WGC) is a proposed constraint on theories with gauge fields and gravity, requiring the existence of light charged particles and/or imposing an upper bound on the field theory cutoff Λ . If taken as a consistency requirement for effective field theories (EFTs), it rules out possibilities for model building including some models of inflation. I demonstrate simple models which satisfy all forms of the WGC, but which through Higgsing of the original gauge fields produce low-energy EFTs with gauge forces that badly violate the WGC. These models illustrate specific loopholes in arguments that motivate the WGC from a bottom-up perspective; for example the arguments based on magnetic monopoles are evaded when the magnetic confinement that occurs in a Higgs phase is accounted for. This indicates that the WGC should not be taken as a veto on EFTs, even if it turns out to be a robust property of UV quantum gravity theories. However, if the latter is true, then parametric violation of the WGC at low energy comes at the cost of nonminimal field content in the UV. I propose that only a very weak constraint is applicable to EFTs, Λ ≲(log 1/g )-1 /2Mpl , where g is the gauge coupling, motivated by entropy bounds. Remarkably, EFTs produced by Higgsing a theory that satisfies the WGC can saturate but not violate this bound.

  17. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  18. Born Level Bound States

    Science.gov (United States)

    Hoyer, Paul

    2017-05-01

    Bound state poles in the S-matrix of perturbative QED are generated by the divergence of the expansion in α . The perturbative corrections are necessarily singular when expanding around free, {O}( α ^0 ) in and out states that have no overlap with finite-sized atomic wave functions. Nevertheless, measurables such as binding energies do have well-behaved expansions in powers of α (and log α ). It is desirable to formulate the concept of "lowest order" for gauge theory bound states such that higher order corrections vanish in the α → 0 limit. This may allow to determine a lowest order term for QCD hadrons which incorporates essential features such as confinement and chiral symmetry breaking, and thus can serve as the starting point of a useful perturbative expansion. I discuss a "Born" (no loop, lowest order in \\hbar ) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. Gauss' law determines a distinct field A^0({\\varvec{x}}) for each instantaneous position of the charges. A Poincaré covariant boundary condition for the gluon field leads to a confining potential for q\\bar{q} and qqq states. In frames where the bound state is in motion the classical gauge field is obtained by a Lorentz boost of the rest frame field.

  19. Weak ferromagnetic behavior, crystal structure, and electronic studies of novel [Cu(II)(Br)(PhCO 2)(Sp)] (Sp=(-)-sparteine) complex

    Science.gov (United States)

    Reyes-Ortega, Yasmi; Alcántara-Flores, José Luis; Hernández-Galindo, María del Carmen; Gutiérrez-Pérez, René; Ramírez-Rosales, Daniel; Bernès, Sylvain; Cabrera-Vivas, Blanca Martha; Durán-Hernández, Alejandro; Zamorano-Ulloa, Rafael

    2006-05-01

    Complex [Cu(II)(Br)(PhCO 2)(Sp)] 1 is obtained starting from copper(0), (-)-sparteine (sp) and benzoyl bromide. 1 Crystallizes in the monoclinic space group P2 1 with a=14.8857(11), b=8.9257(9), c=17.4456(14) Å, β=111.689(5)°, and Z=4. The UV-vis spectrum is characteristic of Cu(II) complexes with tetragonally distorted square pyramidal geometry. The far IR spectrum of 1 shows characteristic vibrations of Cu-Br (239 cm -1), Cu-N (437 cm -1) and Cu-O (466 cm -1) bonds. The 1H NMR broad chemical shifts of 1 integrated for a total of 31 protons and are typical of Cu(II) complexes. ESR spectra of polycrystalline 1 at 77 and 300 K show axial spectra with areas in the ratio A77/ A300=4.02, suggesting a very weak Cu-Cu ferromagnetic interaction. Complex 1-doped with Zn(II) gives hfs with hyperfine interaction constant value A∥=112.45×10 -4 cm -1. The magnetization vs temperature data in the 2-299 K range, show that cupric ion pairs interact through a small antiferromagnetic Heisenberg exchange energy— JS1· S2 with a ground singlet state S=0, separated by J=-1.3 cm -1 from the excited triplet state S=1. The sign of the very weak interchange interaction constant, J, does not agree with the ESR spectra areas ratio of 1 at 77 and 300 K, which is a more accurate quantification of the weak ferromagnetic interaction Cu-Cu through the space.

  20. Upper bounds for domination related parameters in graphs on surfaces

    Directory of Open Access Journals (Sweden)

    Vladimir Samodivkin

    2016-08-01

    Full Text Available In this paper we give tight upper bounds on the total domination number, the weakly connected domination number and the connected domination number of a graph in terms of order and Euler characteristic. We also present upper bounds for the restrained bondage number, the total restrained bondage number and the restricted edge connectivity of graphs in terms of the orientable/nonorientable genus and maximum degree.

  1. On Weak Markov's Principle

    DEFF Research Database (Denmark)

    Kohlenbach, Ulrich Wilhelm

    2002-01-01

    We show that the so-called weak Markov's principle (WMP) which states that every pseudo-positive real number is positive is underivable in E-HA + AC. Since allows one to formalize (atl eastl arge parts of) Bishop's constructive mathematics, this makes it unlikely that WMP can be proved within...

  2. Linear Plotkin bound for entanglement-assisted quantum codes

    Science.gov (United States)

    Guo, Luobin; Li, Ruihu

    2013-03-01

    The entanglement-assisted (EA) formalism is a generalization of the standard stabilizer formalism, and it can transform arbitrary quaternary classical linear codes into entanglement-assisted quantum error correcting codes (EAQECCs) by using of shared entanglement between the sender and the receiver. Using the special structure of linear EAQECCs, we derive an EA-Plotkin bound for linear EAQECCs, which strengthens the previous known EA-Plotkin bound. This linear EA-Plotkin bound is tighter then the EA-Singleton bound, and matches the EA-Hamming bound and the EA-linear programming bound in some cases. We also construct three families of EAQECCs with good parameters. Some of these EAQECCs saturate this linear EA-Plotkin bound and the others are near optimal according to this bound; almost all of these linear EAQECCs are degenerate codes.

  3. The crystal structure of the interleukin 21 receptor bound to interleukin 21 reveals that a sugar chain interacting with the WSXWS motif is an integral part of the interleukin 21 receptor

    DEFF Research Database (Denmark)

    Hamming, Ole Jensen; Kang, Lishan; Svensson, Anders

    2012-01-01

    Interleukin (IL) 21 is a class I cytokine, which exerts pleiotropic effects on both innate and adaptive immune responses. It signals through a heterodimeric receptor complex consisting of the IL-21 receptor (IL-21R) and the common gamma chain (gC). A hallmark of the class I cytokine receptors...... to be a consensus sequence for C-mannosylation. Here we present the crystal structure of IL-21 bound to IL-21R and reveal that the WSXWS motif of IL-21R is C-mannosylated on the first tryptophan. We furthermore demonstrate that a sugar chain bridge the two fibronectin domains which constitute the extracellular...

  4. Composite weak bosons

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, M.

    1988-04-01

    Dynamical mechanism of composite W and Z is studied in a 1/N field theory model with four-fermion interactions in which global weak SU(2) symmetry is broken explicitly by electromagnetic interaction. Issues involved in such a model are discussed in detail. Deviation from gauge coupling due to compositeness and higher order loop corrections are examined to show that this class of models are consistent not only theoretically but also experimentally.

  5. Asymptotic theory of weakly dependent random processes

    CERN Document Server

    Rio, Emmanuel

    2017-01-01

    Presenting tools to aid understanding of asymptotic theory and weakly dependent processes, this book is devoted to inequalities and limit theorems for sequences of random variables that are strongly mixing in the sense of Rosenblatt, or absolutely regular. The first chapter introduces covariance inequalities under strong mixing or absolute regularity. These covariance inequalities are applied in Chapters 2, 3 and 4 to moment inequalities, rates of convergence in the strong law, and central limit theorems. Chapter 5 concerns coupling. In Chapter 6 new deviation inequalities and new moment inequalities for partial sums via the coupling lemmas of Chapter 5 are derived and applied to the bounded law of the iterated logarithm. Chapters 7 and 8 deal with the theory of empirical processes under weak dependence. Lastly, Chapter 9 describes links between ergodicity, return times and rates of mixing in the case of irreducible Markov chains. Each chapter ends with a set of exercises. The book is an updated and extended ...

  6. Silver(I) complexes of the weakly coordinating solvents SO(2) and CH(2)Cl(2): crystal structures, bonding, and energetics of [Ag(OSO)][Al{OC(CF(3))(3)}(4)], [Ag(OSO)(2/2)][SbF(6)], and [Ag(CH(2)Cl(2))(2)][SbF(6)].

    Science.gov (United States)

    Decken, Andreas; Knapp, Carsten; Nikiforov, Grigori B; Passmore, Jack; Rautiainen, J Mikko; Wang, Xinping; Zeng, Xiaoqing

    2009-06-22

    Pushing the limits of coordination chemistry: The most weakly coordinated silver complexes of the very weakly coordinating solvents dichloromethane and liquid sulfur dioxide were prepared. Special techniques at low temperatures and the use of weakly coordinating anions allowed structural characterization of [Ag(OSO)][Al{OC(CF(3))(3)}(4)], [Ag(OSO)(2/2)][SbF(6)], and [Ag(Cl(2)CH(2))(2)][SbF(6)] (see figure). An investigation of the bonding shows that these complexes are mainly stabilized by electrostatic monopole-dipole interactions.The synthetically useful solvent-free silver(I) salt Ag[Al(pftb)(4)] (pftb=--OC(CF(3))(3)) was prepared by metathesis reaction of Li[Al(pftb)(4)] with Ag[SbF(6)] in liquid SO(2). The solvated complexes [Ag(OSO)][Al(pftb)(4)], [Ag(OSO)(2/2)][SbF(6)], and [Ag(CH(2)Cl(2))(2)][SbF(6)] were prepared and isolated by special techniques at low temperatures and structurally characterized by single-crystal X-ray diffraction. The SO(2) complexes provide the first examples of coordination of the very weak Lewis base SO(2) to silver(I). The SO(2) molecule in [Ag(OSO)][Al(pftb)(4)] is eta(1)-O coordinated to Ag(+), while the SO(2) ligands in [Ag(OSO)(2/2)][SbF(6)] bridge two Ag(+) ions in an eta(2)-O,O' (trans,trans) manner. [Ag(CH(2)Cl(2))(2)][SbF(6)] contains [Ag(CH(2)Cl(2))(2)](+) ions linked through [SbF(6)](-) ions to give a polymeric structure. The solid-state silver(I) ion affinities (SIA) of SO(2) and CH(2)Cl(2), based on bond lengths and corresponding valence units in the corresponding complexes and tensimetric titrations of Ag[Al(pftb)(4)] and Ag[SbF(6)] with SO(2) vapor, show that SO(2) is a weaker ligand to Ag(+) than the commonly used weakly coordinating solvent CH(2)Cl(2) and indicated that binding strength of SO(2) to silver(I) in the silver(I) salts increases with increasing size of the corresponding counteranion ([Al(pftb)(4)](-)>[SbF(6)](-)). The experimental findings are in good agreement with theoretical gas-phase ligand

  7. Structures of the Michaelis Complex (1.2A) and the Covalent Acyl Intermediate (2.0A ) of Cefamandole Bound in the Active Sites of the Mycobacterium tuberculosis beta-Lactamase K72A and E166A Mutants

    Energy Technology Data Exchange (ETDEWEB)

    L Tremblay; h Xu; J Blanchard

    2011-12-31

    The genome of Mycobacterium tuberculosis (TB) contains a gene that encodes a highly active {beta}-lactamase, BlaC, that imparts TB with resistance to {beta}-lactam chemotherapy. The structure of covalent BlaC-{beta}-lactam complexes suggests that active site residues K73 and E166 are essential for acylation and deacylation, respectively. We have prepared the K73A and E166A mutant forms of BlaC and have determined the structures of the Michaelis complex of cefamandole and the covalently bound acyl intermediate of cefamandole at resolutions of 1.2 and 2.0 {angstrom}, respectively. These structures provide insight into the details of the catalytic mechanism.

  8. Determination of L-AP4-bound human mGlu8 receptor amino terminal domain structure and the molecular basis for L-AP4's group III mGlu receptor functional potency and selectivity.

    Science.gov (United States)

    Schkeryantz, Jeffery M; Chen, Qi; Ho, Joseph D; Atwell, Shane; Zhang, Aiping; Vargas, Michelle C; Wang, Jing; Monn, James A; Hao, Junliang

    2018-02-15

    L-2-Amino-4-phosphonobutyric acid (L-AP4) is a known potent and selective agonist for the Group III mGlu receptors. However, it does not show any selectivity among the individual group III mGlu subtypes. In order to understand the molecular basis for this group selectivity, we solved the first human mGlu8 amino terminal domain (ATD) crystal structures in complex with L-glu and L-AP4. In comparison with other published L-glu-bound mGlu ATD structures, we have observed L-glu binds in a significantly different manner in mGlu1. Furthermore, these new structures provided evidence that both the electronic and steric nature of the distal phosphate of L-AP4 contribute to its exquisite Group III functional agonist potency and selectivity. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. On the bound state of the antiproton-deuterium-tritium ion

    CERN Document Server

    Frolov, Alexei M

    2012-01-01

    It is shown that the ground state in the Coulomb three-body $\\bar{p}dt$ ion is bound. This ion consists of the positevely charged deuterium $d$ and tritum $t$ nuclei and one negatively charged antirpoton $\\bar{p}$. The $\\bar{p}dt$ ion has only one bound $S(L = 0)-$state which is weakly-bound. The properties of this weakly-bound state are investigated with the use of the results of recent highly accurate computations. Very likely, the actual proparties of the $\\bar{p}dt$ ion will be different from the results of our predictions due to additional contributions from strong interactions between particles.

  10. The Weak Haagerup Property II

    DEFF Research Database (Denmark)

    Haagerup, Uffe; Knudby, Søren

    2015-01-01

    The weak Haagerup property for locally compact groups and the weak Haagerup constant were recently introduced by the second author [27]. The weak Haagerup property is weaker than both weak amenability introduced by Cowling and the first author [9] and the Haagerup property introduced by Connes [6......] and Choda [5]. In this paper, it is shown that a connected simple Lie group G has the weak Haagerup property if and only if the real rank of G is zero or one. Hence for connected simple Lie groups the weak Haagerup property coincides with weak amenability. Moreover, it turns out that for connected simple...... Lie groups the weak Haagerup constant coincides with the weak amenability constant, although this is not true for locally compact groups in general. It is also shown that the semidirect product R2 × SL(2,R) does not have the weak Haagerup property....

  11. Weak self-interactions of globular proteins studied by small-angle X-ray scattering and structure-based modeling

    CERN Document Server

    Kaieda, Shuji; Plivelic, Tomás S; Halle, Bertil

    2014-01-01

    We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty acid-binding protein (IFABP) is determined from SAXS measurements at multiple concentrations, from Monte Carlo simulations with a coarse-grained structure-based interaction model, and from analytic approximate solutions of two idealized colloidal interaction models without adjustable parameters. By combining these approaches, we find that the structure factor is essentially determined by hard-core and screened electrostatic interactions. Other soft short-ranged interactions (van der Waals and solvation-related) are either individually insignificant or tend to cancel out. The structure factor is also not significantly affected by charge fluctuations. For Mb and IFABP, with small net charge and relatively symmetric charge distribution, the structure factor is well described b...

  12. Structure-activity relationships studies on weakly basic N-arylsulfonylindoles with an antagonistic profile in the 5-HT6 receptor

    Science.gov (United States)

    Mella, Jaime; Villegas, Francisco; Morales-Verdejo, César; Lagos, Carlos F.; Recabarren-Gajardo, Gonzalo

    2017-07-01

    We recently reported a series of 39 weakly basic N-arylsulfonylindoles as novel 5-HT6 antagonists. Eight of the compounds exhibited moderate to high binding affinities, with 2-(4-(2-Methoxyphenyl)piperazin-1-yl)-1-(1-tosyl-1H-indol-3-yl)ethanol 16 showing the highest binding affinity (pKi = 7.87). Given these encouraging results and as a continuation of our research, we performed an extensive step-by-step search for the best 3D-QSAR model that allows us to rationally propose novel molecules with improved 5-HT6 affinity based on our previously reported series. A comparative molecular similarity indices analysis (CoMSIA) model built on a docking-based alignment was developed, wherein steric, electrostatic, hydrophobic and hydrogen bond properties are correlated with biological activity. The model was validated internally and externally (q2 = 0.721; r2pred = 0.938), and identified the sulfonyl and hydroxyl groups and the piperazine ring among the main regions of the molecules that can be modified to create new 5-HT6 antagonists.

  13. Dromions bound states

    Energy Technology Data Exchange (ETDEWEB)

    Maccari, Attilio

    2003-03-01

    The asymptotic perturbation (AP) method is applied to the study of the nonlinear Klein-Gordon equation in 3+1 dimensions with harmonic potential and external periodic excitation supposed to be in primary resonance with the frequency of a generic mode. The AP method uses two different procedures for the solutions: introducing an asymptotic temporal rescaling and balancing of the harmonic terms with a simple iteration. Standard quantum mechanics can be used to derive the lowest order approximate solution and amplitude and phase modulation equations are obtained. External force-response and frequency-response curves are found and the existence of dromions trapped in bound states is demonstrated.

  14. Measurement of weak radioactivity

    CERN Document Server

    Theodorsson , P

    1996-01-01

    This book is intended for scientists engaged in the measurement of weak alpha, beta, and gamma active samples; in health physics, environmental control, nuclear geophysics, tracer work, radiocarbon dating etc. It describes the underlying principles of radiation measurement and the detectors used. It also covers the sources of background, analyzes their effect on the detector and discusses economic ways to reduce the background. The most important types of low-level counting systems and the measurement of some of the more important radioisotopes are described here. In cases where more than one type can be used, the selection of the most suitable system is shown.

  15. ICU-Acquired Weakness.

    Science.gov (United States)

    Jolley, Sarah E; Bunnell, Aaron E; Hough, Catherine L

    2016-11-01

    Survivorship after critical illness is an increasingly important health-care concern as ICU use continues to increase while ICU mortality is decreasing. Survivors of critical illness experience marked disability and impairments in physical and cognitive function that persist for years after their initial ICU stay. Newfound impairment is associated with increased health-care costs and use, reductions in health-related quality of life, and prolonged unemployment. Weakness, critical illness neuropathy and/or myopathy, and muscle atrophy are common in patients who are critically ill, with up to 80% of patients admitted to the ICU developing some form of neuromuscular dysfunction. ICU-acquired weakness (ICUAW) is associated with longer durations of mechanical ventilation and hospitalization, along with greater functional impairment for survivors. Although there is increasing recognition of ICUAW as a clinical entity, significant knowledge gaps exist concerning identifying patients at high risk for its development and understanding its role in long-term outcomes after critical illness. This review addresses the epidemiologic and pathophysiologic aspects of ICUAW; highlights the diagnostic challenges associated with its diagnosis in patients who are critically ill; and proposes, to our knowledge, a novel strategy for identifying ICUAW. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

  16. Synthesis and application of new polymer bound catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Fetterly, Brandon Michael [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    Nitric acid has been shown to be a weak acid in acetonitrile. It is conceivable that a nitrate salt of a weakly Lewis acidic cation could furnish a ''naked'' nitrate anion as a basic catalyst in a variety of reactions in non-aqueous solvents. Such a nitrate salt could also be bound to a polymeric support via the cation, thereby allowing for reclamation and recycling of the nitrate ion. This subject is dealt with in Chapter 2, wherein my contributions consisted of performing all the reactions with the polymer supported catalyst and carrying out the experiments necessary to shed light on the reaction mechanisms. Chapter 3 contains a description of the structure and catalytic properties of an azidoproazaphosphatrane. This compound is an air-stable versatile catalyst that has proven useful not only homogeneously, but also when bound to a solid support. The synthesis of a polymer bound proazaphosphatrane containing a trivalent phosphorus is presented in Chapter 4. Such a compound has been sought after by our group for a number of years. Not only does the synthesis I have accomplished for it allow for easier separation of proazaphosphatrane catalysts from reaction mixtures, but recycling of the base is made much simpler. Proazaphosphatranes are useful homogeneous catalysts that activate atoms in other reagents, thus enhancing their reactivity. The next chapters deal with two such reactions with aldehydes and ketones, namely silylcyanations with trialkylsilylcyanides (Chapters 5 and 6) and reductions with poly(methylhydrosiloxane), in Chapter 7. In Chapter 5, Zhigang Wang performed the initial optimization and scoping of the reaction, while repetitions of the scoping experiments for reproducibility, determination of diastereomeric ratios, and experiments aimed at elucidating aspects of the mechanism were performed by me. The proazaphosphatrane coordinates to the silicon atom in both cases, thereby allowing the aforementioned reactions to proceed under

  17. Structure and Dynamic Properties of a Ti-Binding Peptide Bound to TiO2 Nanoparticles As Accessed by (1)H NMR Spectroscopy.

    Science.gov (United States)

    Suzuki, Yu; Shindo, Heisaburo; Asakura, Tetsuo

    2016-05-26

    Saturation transfer difference (STD) NMR spectroscopy is a powerful method for detecting and characterizing ligand-receptor interactions. In this study, the STD method was used to characterize the interactions of a Ti-binding peptide (TBP:RKLPDA) with TiO2 nanoparticles. The water peak in the NMR spectrum was selectively saturated, and the STD amplitudes for TBP were observed in the presence of TiO2, demonstrating that the side chains of the N-terminal residues Arg1 and Lys2 exhibit the strongest saturation transfer effect from water molecules; i.e., the two N-terminal residues are in contact with the TiO2 surface. The relaxation rate in the rotating frame, R1ρ, was observed to be high at the N-terminal residues; R1ρ decelerated toward the C-terminus, indicating that the N-terminal residues serve as anchors on the TiO2 surface and that the TBP motion bound to TiO2 particles is modeled as a wobble-in-cone with a fairly flexible C-terminus. The dissociation constant Kd of the TBP-TiO2 nanoparticle complex was 4.9 ± 1.8 mM, as estimated from the STD experiments and R1ρ measurements. The combination of these results and the negative zeta potential of the TiO2 surface validate that both the positively charged guanidyl group of Arg1 and amino group of Lys2 play key roles in interaction with the TiO2 surface by electrostatic force.

  18. Crystal structure of the high-affinity Na+,K+-ATPase–ouabain complex with Mg2+ bound in the cation binding site

    DEFF Research Database (Denmark)

    Laursen, Mette; Yatime, Laure; Nissen, Poul

    2013-01-01

    of ouabain and the side chains of αM1, αM2, and αM6. Furthermore, the structure reveals that cation transport site II is occupied by Mg2+, and crystallographic studies indicate that Rb+ and Mn2+, but not Na+, bind to this site. Comparison with the low-affinity [K2]E2–MgFx–ouabain structure [Ogawa et al...

  19. Vulnerable Derivatives and Good Deal Bounds

    DEFF Research Database (Denmark)

    Murgoci, Agatha

    2013-01-01

    We price vulnerable derivatives – i.e. derivatives where the counterparty may default. These are basically the derivatives traded on the over-the-counter (OTC) markets. Default is modelled in a structural framework. The technique employed for pricing is good deal bounds (GDBs). The method imposes...

  20. Refining Multivariate Value Set Bounds

    Science.gov (United States)

    Smith, Luke Alexander

    Over finite fields, if the image of a polynomial map is not the entire field, then its cardinality can be bounded above by a significantly smaller value. Earlier results bound the cardinality of the value set using the degree of the polynomial, but more recent results make use of the powers of all monomials. In this paper, we explore the geometric properties of the Newton polytope and show how they allow for tighter upper bounds on the cardinality of the multivariate value set. We then explore a method which allows for even stronger upper bounds, regardless of whether one uses the multivariate degree or the Newton polytope to bound the value set. Effectively, this provides an alternate proof of Kosters' degree bound, an improved Newton polytope-based bound, and an improvement of a degree matrix-based result given by Zan and Cao.

  1. Weak Quantum Ergodicity

    CERN Document Server

    Kaplan, L

    1998-01-01

    We examine the consequences of classical ergodicity for the localization properties of individual quantum eigenstates in the classical limit. We note that the well known Schnirelman result is a weaker form of quantum ergodicity than the one implied by random matrix theory. This suggests the possibility of systems with non-gaussian random eigenstates which are nonetheless ergodic in the sense of Schnirelman and lead to ergodic transport in the classical limit. These we call "weakly quantum ergodic.'' Indeed for a class of "slow ergodic" classical systems, it is found that each eigenstate becomes localized to an ever decreasing fraction of the available state space, in the semiclassical limit. Nevertheless, each eigenstate in this limit covers phase space evenly on any classical scale, and long-time transport properties betwen individual quantum states remain ergodic due to the diffractive effects which dominate quantum phase space exploration.

  2. The crystal structure of the calcium-bound con-G[Q6A] peptide reveals a novel metal-dependent helical trimer

    Energy Technology Data Exchange (ETDEWEB)

    Cnudde, Sara E.; Prorok, Mary; Jia, Xaofei; Castellino, Francis J.; Geiger, James H. (MSU); (Notre)

    2012-02-15

    The ability to form and control both secondary structure and oligomerization in short peptides has proven to be challenging owing to the structural instability of such peptides. The conantokin peptides are a family of {gamma}-carboxyglutamic acid containing peptides produced in the venoms of predatory sea snails of the Conus family. They are examples of short peptides that form stable helical structures, especially in the presence of divalent cations. Both monomeric and dimeric conantokin peptides have been identified and represent a new mechanism of helix association, 'the metallozipper motif' that is devoid of a hydrophobic interface between monomers. In the present study, a parallel/antiparallel three-helix bundle was identified and its crystal structure determined at high resolution. The three helices are almost perfectly parallel and represent a novel helix-helix association. The trimer interface is dominated by metal chelation between the three helices, and contains no interfacial hydrophobic interactions. It is now possible to produce stable monomeric, dimeric, or trimeric metallozippers depending on the peptide sequence and metal ion. Such structures have important applications in protein design.

  3. Crystal Structure of Fatty Acid Amide Hydrolase Bound to the Carbamate Inhibitor URB597: Discovery of a Deacylating Water Molecule and Insight into Enzyme Inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Mileni, Mauro; Kamtekar, Satwik; Wood, David C.; Benson, Timothy E.; Cravatt, Benjamin F.; Stevens, Raymond C. (Scripps); (Pfizer)

    2010-08-12

    The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 {angstrom} resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 {angstrom}) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases.

  4. Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1

    Energy Technology Data Exchange (ETDEWEB)

    Gwon, Gwang Hyeon; Kim, Youngran; Liu, Yaqi; Watson, Adam T.; Jo, Aera; Etheridge, Thomas J.; Yuan, Fenghua; Zhang, Yanbin; Kim, YoungChang; Carr, Anthony M.; Cho, Yunje

    2014-10-15

    Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI–FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

  5. Insight into the PrPC-->PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants.

    Science.gov (United States)

    Eghiaian, Frédéric; Grosclaude, Jeanne; Lesceu, Stéphanie; Debey, Pascale; Doublet, Bénédicte; Tréguer, Eric; Rezaei, Human; Knossow, Marcel

    2004-07-13

    Prion diseases are associated with the conversion of the alpha-helix rich prion protein (PrPC) into a beta-structure-rich insoluble conformer (PrPSc) that is thought to be infectious. The mechanism for the PrPC-->PrPSc conversion and its relationship with the pathological effects of prion diseases are poorly understood, partly because of our limited knowledge of the structure of PrPSc. In particular, the way in which mutations in the PRNP gene yield variants that confer different susceptibilities to disease needs to be clarified. We report here the 2.5-A-resolution crystal structures of three scrapie-susceptibility ovine PrP variants complexed with an antibody that binds to PrPC and to PrPSc; they identify two important features of the PrPC-->PrPSc conversion. First, the epitope of the antibody mainly consists of the last two turns of ovine PrP second alpha-helix. We show that this is a structural invariant in the PrPC-->PrPSc conversion; taken together with biochemical data, this leads to a model of the conformational change in which the two PrPC C-terminal alpha-helices are conserved in PrPSc, whereas secondary structure changes are located in the N-terminal alpha-helix. Second, comparison of the structures of scrapie-sensitivity variants defines local changes in distant parts of the protein that account for the observed differences of PrPC stability, resistant variants being destabilized compared with sensitive ones. Additive contributions of these sensitivity-modulating mutations to resistance suggest a possible causal relationship between scrapie resistance and lowered stability of the PrP protein.

  6. Core-shell structured polystyrene/BaTiO3 hybrid nanodielectrics prepared by in situ RAFT polymerization: a route to high dielectric constant and low loss materials with weak frequency dependence.

    Science.gov (United States)

    Yang, Ke; Huang, Xingyi; Xie, Liyuan; Wu, Chao; Jiang, Pingkai; Tanaka, Toshikatsu

    2012-11-23

    A novel route to prepare core-shell structured nanocomposites with excellent dielectric performance is reported. This approach involves the grafting of polystyrene (PS) from the surface of BaTiO(3) by an in situ RAFT polymerization. The core-shell structured PS/BaTiO(3) nanocomposites not only show significantly increased dielectric constant and very low dielectric loss, but also have a weak frequency dependence of dielectric properties over a wide range of frequencies. In addition, the dielectric constant of the nanocomposites can also be easily tuned by varying the thickness of the PS shell. Our method is very promising for preparing high-performance nanocomposites used in energy-storage devices. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Structure and magnetism in Fe-Gd based dinuclear and chain systems: the interplay of weak exchange coupling and zero field splitting effects

    NARCIS (Netherlands)

    Ferbinteanu, M.; Cimpoesu, F.; Gîrtu, M. A.; Enachescu, C.; Tanase, S.

    2012-01-01

    The synthesis and characterization of two Fe-Gd systems based on bpca- (Hbpca = bis(2-pyridilcarbonyl)amine) as bridging ligand is presented, taking the systems as a case study for structure-property correlations. Compound 1, [FeLSII(μ-bpca)2Gd(NO3)2(H2O)]NO3·2CH3NO2, is a zigzag polymer,

  8. Fibered Transverse Knots and the Bennequin Bound

    OpenAIRE

    Etnyre, John B.; Van Horn-Morris, Jeremy

    2008-01-01

    We prove that a nicely fibered link (by which we mean the binding of an open book) in a tight contact manifold $(M,\\xi)$ with zero Giroux torsion has a transverse representative realizing the Bennequin bound if and only if the contact structure it supports (since it is also the binding of an open book) is $\\xi.$ This gives a geometric reason for the non-sharpness of the Bennequin bound for fibered links. We also note that this allows the classification, up to contactomorphism, of maximal self...

  9. A site of varicella-zoster virus vulnerability identified by structural studies of neutralizing antibodies bound to the glycoprotein complex gHgL.

    Science.gov (United States)

    Xing, Yi; Oliver, Stefan L; Nguyen, TuongVi; Ciferri, Claudio; Nandi, Avishek; Hickman, Julie; Giovani, Cinzia; Yang, Edward; Palladino, Giuseppe; Grose, Charles; Uematsu, Yasushi; Lilja, Anders E; Arvin, Ann M; Carfí, Andrea

    2015-05-12

    Varicella-zoster virus (VZV), of the family Alphaherpesvirinae, causes varicella in children and young adults, potentially leading to herpes zoster later in life on reactivation from latency. The conserved herpesvirus glycoprotein gB and the heterodimer gHgL mediate virion envelope fusion with cell membranes during virus entry. Naturally occurring neutralizing antibodies against herpesviruses target these entry proteins. To determine the molecular basis for VZV neutralization, crystal structures of gHgL were determined in complex with fragments of antigen binding (Fabs) from two human monoclonal antibodies, IgG-94 and IgG-RC, isolated from seropositive subjects. These structures reveal that the antibodies target the same site, composed of residues from both gH and gL, distinct from two other neutralizing epitopes identified by negative-stain electron microscopy and mutational analysis. Inhibition of gB/gHgL-mediated membrane fusion and structural comparisons with herpesvirus homologs suggest that the IgG-RC/94 epitope is in proximity to the site on VZV gHgL that activates gB. Immunization studies proved that the anti-gHgL IgG-RC/94 epitope is a critical target for antibodies that neutralize VZV. Thus, the gHgL/Fab structures delineate a site of herpesvirus vulnerability targeted by natural immunity.

  10. Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501

    DEFF Research Database (Denmark)

    Røder, Gustav; Kristensen, Ole; Kastrup, Jette S

    2008-01-01

    , the crystal structure of HLA-B*1501 in complex with a SARS coronavirus-derived nonapeptide (VQQESSFVM) has been determined at high resolution (1.87 A). The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making...

  11. The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase.

    Science.gov (United States)

    Amaya, Maria Fernanda; Buschiazzo, Alejandro; Nguyen, Tong; Alzari, Pedro M

    2003-01-24

    The structure of the recombinant Trypanosoma rangeli sialidase (TrSA) has been determined at 1.6A resolution, and the structures of its complexes with the transition state analog inhibitor 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (DANA), Neu-5-Ac-thio-alpha(2,3)-galactoside (NATG) and N-acetylneuraminic acid (NANA) have been determined at 1.64A, 2.1A and 2.85A, respectively. The 3D structure of TrSA is essentially identical to that of the natural enzyme, except for the absence of covalently attached sugar at five distinct N-glycosylation sites. The protein exhibits a topologically rigid active site architecture that is unaffected by ligand binding. The overall binding of DANA to the active site cleft is similar to that observed for other viral and bacterial sialidases, dominated by the interactions of the inhibitor carboxylate with the conserved arginine triad. However, the interactions of the other pyranoside ring substituents (hydroxyl, N-acetyl and glycerol moieties) differ between trypanosomal, bacterial and viral sialidases, providing a structural basis for specific inhibitor design. Sialic acid is found to bind the enzyme with the sugar ring in a distorted (half-chair or boat) conformation and the 2-OH hydroxyl group at hydrogen bonding distance of the carboxylate of Asp60, substantiating a direct catalytic role for this residue. A detailed comparison of TrSA with the closely related structure of T.cruzi trans-sialidase (TcTS) reveals a highly conserved catalytic center, where subtle structural differences account for strikingly different enzymatic activities and inhibition properties. The structure of TrSA in complex with NATG shows the active site cleft occupied by a smaller compound which could be identified as DANA, probably the product of a hydrolytic side reaction. Indeed, TrSA (but not TcTS) was found to cleave O and S-linked sialylated substrates, further stressing the functional differences between trypanosomal sialidases and trans-sialidases.

  12. Withering away, weakly

    NARCIS (Netherlands)

    F.A. Muller (Archibald)

    2011-01-01

    textabstractOne of the reasons provided for the shift away from an ontology for physical reality of material objects & properties towards one of physical structures & relations (Ontological Structural Realism: OntSR) is that the quantum-mechanical description of composite physical systems of similar

  13. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.; Yale

    2009-06-30

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the Asite cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  14. U2504 Determines the Species Specificity of the A-site Cleft Antibiotics: The sStructures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gurel, G.; Blaha, G; Moore, P; Steitz,

    2009-01-01

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  15. Dataset for the NMR structure of the intrinsically disordered acidic region of XPC bound to the PH domain of TFIIH p62

    Directory of Open Access Journals (Sweden)

    Masahiko Okuda

    2016-03-01

    Full Text Available The global genome nucleotide excision repair factor XPC firstly detects DNA lesions and then recruits a ten-subunit complex TFIIH through binding to the subunit p62 to unwind the damaged DNA for excision repair. This data article contains detailed nuclear magnetic resonance (NMR restraints (nuclear Overhauser enhancement (NOE-derived distance restraints, dihedral angle restraints, and hydrogen bond restraints used for the structure determination of the complex formed between the intrinsically disordered acidic region of XPC and the pleckstrin homology (PH domain of TFIIH p62, related to the recent work entitled “Structural insight into the mechanism of TFIIH recognition by the acidic string of the nucleotide excision repair factor XPC.” [1].

  16. Muscle weakness causes joint degeneration in rabbits.

    Science.gov (United States)

    Rehan Youssef, A; Longino, D; Seerattan, R; Leonard, T; Herzog, W

    2009-09-01

    The objective of this study was to investigate the effects of botulinum toxin type-A (BTX-A) induced quadriceps weakness on micro-structural changes in knee cartilage of New Zealand White (NZW) rabbits. Fifteen rabbits were divided randomly into an experimental and a sham control group. Each group received a unilateral single quadriceps muscle injection either with saline (sham control; n=4) or BTX-A (experimental; n=11). BTX-A injection produced significant quadriceps muscle weakness (Pmuscle mass (Pknee cartilage, assessed with the Mankin grading system, were the same for the injected and non-injected hind limbs of the experimental group animals. Sham injection had no effect on joint degeneration but all control animals showed some degenerative changes in the knee. Degenerative changes of the retro-patellar cartilage were more severe in the experimental compared to sham control group rabbits (P0.05). Quadriceps muscle weakness caused increased degeneration in the retro-patellar cartilage of NZW rabbits, providing evidence that muscle weakness might be a risk factor for the onset and progression of osteoarthritis (OA). Future work needs to delineate whether muscle weakness directly affects joint degeneration, or if changes in function and movement execution associated with muscle weakness are responsible for the increased rate of OA onset and progression observed here.

  17. [Potential of cooperative learning in project development : Relevance of cooperative participation procedure for the further development of generation-appropriate accomodation in structurally weak rural areas].

    Science.gov (United States)

    Kaufmann, Gerd; Frankenberg, Olga; Sommer, Ralf-Rüdiger; Jost, Annemarie

    2017-04-01

    A joint initiative of existing senior care organizations, the municipality of Meyenburg and the state of Brandenburg was further developed by affiliation of an institute of the Brandenburg University of Technology Cottbus-Senftenberg (ABV) in cooperation with members of the architecture and social work departments in 2014. A cooperative process between different players was central to create an appropriate structure of services for this region. Cooperative projects are necessary to establish new forms of generation-appropriate living and care concepts in rural areas. Cooperative learning methods are needed to develop new forms of generation-appropriate living and care concepts in rural areas, which take the diversity of elderly people, the rural context, intergenerational residential arrangements and affordable accommodation that meets the requirements of the social security system into account. Furthermore, the project had to reflect the recent developments of the German care insurance. The article describes the participatory methods, the coordination process and the resulting concept.

  18. A measurement of the V-A x V-A structure of the weak charged current in semileptonic b decays and missing energy measurements

    CERN Document Server

    Behner, Frank

    1995-01-01

    The polarization of the W-propagator in semileptonic b decays is measured with the 13 experiment at LEP via simultaneous observation of the charged lepton and the neutrino spectrum. The polarization is seen with more than 3 standard deviations and found to be in agreement with the V-AxV-A structure. The measurement excludes the V+Ax V-A polarization with more than 6 standard deviations. Furthermore, the branching ratio in B_, vX is measured and found to be 22.7%±0.8%(stat.)±l.5%(syst.) which corresponds to a branching ratio of B_,evX of 10.1%±0.8%.

  19. Structural Changes of Zn(IIbleomycin Complexes When Bound to DNA Hairpins Containing the 5′-GT-3′ and 5′-GC-3′ Binding Sites, Studied through NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Shelby E. Follett

    2017-12-01

    Full Text Available We have previously investigated the diverse levels of disruption caused by Zn(IIBLMs with different C-termini to DNA hairpins containing 5′-GC-3′ and 5′-GT-3′ binding sites. The results of this investigation indicated that both the DNA-binding site and the bleomycin C-termini have an impact on the final conformation of the aforementioned hairpins in the drug-target complexes, as suggested by the different sets of intramolecular NOEs displayed by both oligonucleotides when bound to each Zn(IIBLM. The NMR signals elicited by 1H nuclei in the oligonucleotide bases and sugar moieties were also affected differently (shifted upfield or downfield in various patterns depending on the BLM C-termini and the binding site in the oligonucleotides. The overall conclusion derived from the precedent research is that the spatial conformation of target DNA segments in DNA-Zn(IIBLM complexes could be forged by interactions between drug and DNA that are guided by the DNA binding site and the BLM C-termini. The present study focuses on the structural alterations exhibited by Zn(IIbleomycin-A2, -B2, -A5 and Zn(IIpeplomycin molecules upon binding to the previously studied hairpins. Our main goal is to determine if different spatial conformations of the drugs in their DNA-bound forms are found in drug-DNA complexes that differ in the oligonucleotide binding site and BLM C-termini. Evidence that suggest that each Zn(IIbleomycin is structurally affected depending these two factors, as indicated by different sets of intramolecular NOE connectivities between drug protons and diverse patterns of shifting of their 1H-NMR signals, is provided.

  20. Bounding approaches to system identification

    CERN Document Server

    Norton, John; Piet-Lahanier, Hélène; Walter, Éric

    1996-01-01

    In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.

  1. with Bounded Failure Intensity

    Directory of Open Access Journals (Sweden)

    Preeti Wanti Srivastava

    2011-01-01

    Full Text Available This paper deals with the Bayes prediction of the future failures of a deteriorating repairable mechanical system subject to minimal repairs and periodic overhauls. To model the effect of overhauls on the reliability of the system a proportional age reduction model is assumed and the 2-parameter Engelhardt-Bain process (2-EBP is used to model the failure process between two successive overhauls. 2-EBP has an advantage over Power Law Process (PLP models. It is found that the failure intensity of deteriorating repairable systems attains a finite bound when repeated minimal repair actions are combined with some overhauls. If such a data is analyzed through models with unbounded increasing failure intensity, such as the PLP, then pessimistic estimates of the system reliability will arise and incorrect preventive maintenance policy may be defined. On the basis of the observed data and of a number of suitable prior densities reflecting varied degrees of belief on the failure/repair process and effectiveness of overhauls, the prediction of the future failure times and the number of failures in a future time interval is found. Finally, a numerical application is used to illustrate the advantages from overhauls and sensitivity analysis of the improvement parameter carried out.

  2. Mapping the structural requirements of inducers and substrates for decarboxylation of weak acid preservatives by the food spoilage mould Aspergillus niger.

    Science.gov (United States)

    Stratford, Malcolm; Plumridge, Andrew; Pleasants, Mike W; Novodvorska, Michaela; Baker-Glenn, Charles A G; Pattenden, Gerald; Archer, David B

    2012-07-16

    Moulds are able to cause spoilage in preserved foods through degradation of the preservatives using the Pad-decarboxylation system. This causes, for example, decarboxylation of the preservative sorbic acid to 1,3-pentadiene, a volatile compound with a kerosene-like odour. Neither the natural role of this system nor the range of potential substrates has yet been reported. The Pad-decarboxylation system, encoded by a gene cluster in germinating spores of the mould Aspergillus niger, involves activity by two decarboxylases, PadA1 and OhbA1, and a regulator, SdrA, acting pleiotropically on sorbic acid and cinnamic acid. The structural features of compounds important for the induction of Pad-decarboxylation at both transcriptional and functionality levels were investigated by rtPCR and GCMS. Sorbic and cinnamic acids served as transcriptional inducers but ferulic, coumaric and hexanoic acids did not. 2,3,4,5,6-Pentafluorocinnamic acid was a substrate for the enzyme but had no inducer function; it was used to distinguish induction and competence for decarboxylation in combination with the analogue chemicals. The structural requirements for the substrates of the Pad-decarboxylation system were probed using a variety of sorbic and cinnamic acid analogues. High decarboxylation activity, ~100% conversion of 1mM substrates, required a mono-carboxylic acid with an alkenyl double bond in the trans (E)-configuration at position C2, further unsaturation at C4, and an overall molecular length between 6.5Å and 9Å. Polar groups on the phenyl ring of cinnamic acid abolished activity (no conversion). Furthermore, several compounds were shown to block Pad-decarboxylation. These compounds, primarily aldehyde analogues of active substrates, may serve to reduce food spoilage by moulds such as A. niger. The possible ecological role of Pad-decarboxylation of spore self-inhibitors is unlikely and the most probable role for Pad-decarboxylation is to remove cinnamic acid-type inhibitors from

  3. Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole.

    Science.gov (United States)

    Asztalos, Peter; Müller, Astrid; Hölke, Werner; Sobek, Harald; Rudolph, Markus G

    2014-07-01

    Lysobacter enzymogenes lysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a related lysyl endoproteinase from Achromobacter lyticus has favourable enzymatic properties that might be transferrable to LysC. To visualize structural differences in the substrate-binding sites, the crystal structures of wild-type and the K30R variant of LysC were determined. The mutation is located at a distance of 12 Å from the catalytic triad and subtly changes the surface properties of the substrate-binding site. The high pH optimum of LysC can be attributed to electrostatic effects of an aromatic Tyr/His stack on the catalytic aspartate and is a general feature of this enzyme subfamily. LysC crystals in complex with the covalent inhibitor N(α)-p-tosyl-lysyl chloromethylketone yielded data to 1.1 and 0.9 Å resolution, resulting in unprecedented precision of the active and substrate-binding sites for this enzyme subfamily. Error estimates on bond lengths and difference electron density indicate that instead of the expected oxyanion a hydroxyl group binds to the partially solvent-exposed oxyanion hole. Protonation of the alkoxide catalytic intermediate might be a recurring feature during serine protease catalysis.

  4. The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly

    Science.gov (United States)

    Razi, Aida; Guarné, Alba; Ortega, Joaquin

    2017-01-01

    Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit. PMID:28396444

  5. X-ray Crystal Structure of Teicoplanin A2-2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy

    Science.gov (United States)

    2015-01-01

    We report the X-ray crystal structure of a site-selective peptide catalyst moiety and teicoplanin A2-2 complex. The expressed protein ligation technique was used to couple T4 lysozyme (T4L) and a synthetic peptide catalyst responsible for the selective phosphorylation of the N-acetylglucosamine sugar in a teicoplanin A2-2 derivative. The T4L-Pmh-dPro-Aib-dAla-dAla construct was crystallized in the presence of teicoplanin A2-2. The resulting 2.3 Å resolution protein–peptide–teicoplanin complex crystal structure revealed that the nucleophilic nitrogen of N-methylimidazole in the Pmh residue is in closer proximity (7.6 Å) to the N-acetylglucosamine than the two other sugar rings present in teicoplanin (9.3 and 20.3 Å, respectively). This molecular arrangement is consistent with the observed selectivity afforded by the peptide-based catalyst when it is applied to a site-selective phosphorylation reaction involving a teicoplanin A2-2 derivative. PMID:25147913

  6. Transverse-momentum correlations and impact-parameter bounds for exclusive K/sup +/p reactions at 32 GeV/c

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, E.A.; Gysen, M.; Tavernier, S.; Verbeure, F.; Ajinenko, I.V.; Chliapnikov, P.V.; Gerdyukov, L.N.; Lugovsky, S.B.; Riadovikov, V.N.; Rybin, A.M.; Tchikilev, O.G.; Vorobjev, A.B.; Dujardin, C.; Grard, F.; Laurent, J.; De Beer, M.; Laugier, J.P.

    1979-03-01

    The Webber and Henyey-Pumplin lower bounds on the root-mean-square impact parameter of exclusive K/sup +/p reactions are determined and compared with the slope of the overlap function calculated from uncorrelated-particle-production models. The similarity of the lower bounds obtained with different methods is shown to be a consequence of the nearly Gaussian transverse-momentum structure of the reaction matrix element squared at fixed rapidities. Multiplicity and total-energy dependence follow naturally from the dynamical transverse-momentum limitation and phase space. The weakness of the lower bounds constitutes evidence for important phase and/or spin contributions to the average squared impact parameter.

  7. Improved Space Bounds for Cache-Oblivious Range Reporting

    DEFF Research Database (Denmark)

    Afshani, Peyman; Zeh, Norbert

    2011-01-01

    second main result shows that any cache-oblivious 2-d three-sided range reporting data structure with the optimal query bound has to use Ω(N logε N) space, thereby improving on a recent lower bound for the same problem. Using known transformations, the lower bound extends to 3-d dominance reporting and 3......We provide improved bounds on the size of cacheoblivious range reporting data structures that achieve the optimal query bound of O(logB N + K/B) block transfers. Our first main result is an O(N √ logN log logN)-space data structure that achieves this query bound for 3-d dominance reporting and 2-d...... three-sided range reporting. No cache-oblivious o(N log N/ log logN)-space data structure for these problems was known before, even when allowing a query bound of O(logO(1) 2 N + K/B) block transfers.1 Our result also implies improved space bounds for general 2-d and 3-d orthogonal range reporting. Our...

  8. Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Youngchang; Makowska-Grzyska, Magdalena; Gorla, Suresh Kumar; Gollapalli, Deviprasad R.; Cuny, Gregory D.; Joachimiak, Andrzej; Hedstrom, Lizbeth

    2015-04-21

    Inosine 5'-monophosphate dehydrogenase (IMPDH) is a promising target for the treatment ofCryptosporidiuminfections. Here, the structure ofC. parvumIMPDH (CpIMPDH) in complex with inosine 5'-monophosphate (IMP) and P131, an inhibitor within vivoanticryptosporidial activity, is reported. P131 contains two aromatic groups, one of which interacts with the hypoxanthine ring of IMP, while the second interacts with the aromatic ring of a tyrosine in the adjacent subunit. In addition, the amine and NO2moieties bind in hydrated cavities, forming water-mediated hydrogen bonds to the protein. The design of compounds to replace these water molecules is a new strategy for the further optimization ofC. parvuminhibitors for both antiparasitic and antibacterial applications.

  9. Crystal Structures of Multicopper Oxidase CueO Bound to Copper(I) and Silver(I): Functional Role of a Methonine-Rich Sequence

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Satish K.; Roberts, Sue A.; McDevitt, Sylvia F.; Weichsel, Andrzej; Wildner, Guenter F.; Grass, Gregor B.; Rensing, Christopher; Montfort, William R. (Skidmore); (Bundeswehr); (Ariz)

    2011-10-24

    The multicopper oxidase CueO oxidizes toxic Cu(I) and is required for copper homeostasis in Escherichia coli. Like many proteins involved in copper homeostasis, CueO has a methionine-rich segment that is thought to be critical for copper handling. How such segments function is poorly understood. Here, we report the crystal structure of CueO at 1.1 {angstrom} with the 45-residue methionine-rich segment fully resolved, revealing an N-terminal helical segment with methionine residues juxtaposed for Cu(I) ligation and a C-terminal highly mobile segment rich in methionine and histidine residues. We also report structures of CueO with a C500S mutation, which leads to loss of the T1 copper, and CueO with six methionines changed to serine. Soaking C500S CueO crystals with Cu(I), or wild-type CueO crystals with Ag(I), leads to occupancy of three sites, the previously identified substrate-binding site and two new sites along the methionine-rich helix, involving methionines 358, 362, 368, and 376. Mutation of these residues leads to a {approx}4-fold reduction in kcat for Cu(I) oxidation. Ag(I), which often appears with copper in nature, strongly inhibits CueO oxidase activities in vitro and compromises copper tolerance in vivo, particularly in the absence of the complementary copper efflux cus system. Together, these studies demonstrate a role for the methionine-rich insert of CueO in the binding and oxidation of Cu(I) and highlight the interplay among cue and cus systems in copper and silver homeostasis.

  10. ExtremeBounds: Extreme Bounds Analysis in R

    Directory of Open Access Journals (Sweden)

    Marek Hlavac

    2016-08-01

    Full Text Available This article introduces the R package ExtremeBounds to perform extreme bounds analysis (EBA, a sensitivity test that examines how robustly the dependent variable of a regression model is related to a variety of possible determinants. ExtremeBounds supports Leamer's EBA that focuses on the upper and lower extreme bounds of regression coefficients, as well as Sala-i-Martin's EBA which considers their entire distribution. In contrast to existing alternatives, it can estimate models of a variety of user-defined sizes, use regression models other than ordinary least squares, incorporate non-linearities in the model specification, and apply custom weights and standard errors. To alleviate concerns about the multicollinearity and conceptual overlap of examined variables, ExtremeBounds allows users to specify sets of mutually exclusive variables, and can restrict the analysis to coefficients from regression models that yield a variance inflation factor within a prespecified limit.

  11. How much do incentives affect car purchase? Agent-based microsimulation of consumer choice of new cars. Part 1. Model structure, simulation of bounded rationality, and model validation

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Michel G.; Haan, Peter de [ETH Zurich, Institute for Environmental Decisions, Natural and Social Science Interface, Universitaetstr. 22, CHN J 73.2, 8092 Zurich (Switzerland)

    2009-03-15

    This article presents an agent-based microsimulation capable of forecasting the effects of policy levers that influence individual choices of new passenger cars. The fundamental decision-making units are households distinguished by sociodemographic characteristics and car ownership. A two-stage model of individual decision processes is employed. In the first stage, individual choice sets are constructed using simple, non-compensatory rules that are based on previously owned cars. Second, decision makers evaluate alternatives in their individual choice set using a multi-attributive weighting rule. The attribute weights are based on a multinomial logit model for cross-country policy analysis in European countries. Additionally, prospect theory and the notion of mental accounting are used to model the perception of monetary values. The microsimulation forecasts actual market observations with high accuracy, both on the level of aggregate market characteristics as well as on a highly resolved level of distributions of market shares. The presented approach is useful for the assessment of policies that influence individual purchase decisions of new passenger cars; it allows accounting for a highly resolved car fleet and differentiated consumer segments. As a result, the complexity of incentive schemes can be represented and detailed structural changes can be investigated. (author)

  12. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole

    Energy Technology Data Exchange (ETDEWEB)

    Schroeder,S.; Blaha, G.; Tirado-Rives, J.; Steitz, T.; Moore, P.

    2007-01-01

    Crystal structures of the 50 S ribosomal subunit from Haloarcula marismortui complexed with two antibiotics have identified new sites at which antibiotics interact with the ribosome and inhibit protein synthesis. 13-Deoxytedanolide binds to the E site of the 50 S subunit at the same location as the CCA of tRNA, and thus appears to inhibit protein synthesis by competing with deacylated tRNAs for E site binding. Girodazole binds near the E site region, but is somewhat buried and may inhibit tRNA binding by interfering with conformational changes that occur at the E site. The specificity of 13-deoxytedanolide for eukaryotic ribosomes is explained by its extensive interactions with protein L44e, which is an E site component of archaeal and eukaryotic ribosomes, but not of eubacterial ribosomes. In addition, protein L28, which is unique to the eubacterial E site, overlaps the site occupied by 13-deoxytedanolide, precluding its binding to eubacterial ribosomes. Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria.

  13. Building high-coverage monolayers of covalently bound magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Mackenzie G.; Teplyakov, Andrew V., E-mail: andrewt@udel.edu

    2016-12-01

    Graphical abstract: - Highlights: • A method for forming a layer of covalently bound nanoparticles is offered. • A nearly perfect monolayer of covalently bound magnetic nanoparticles was formed on gold. • Spectroscopic techniques confirmed covalent binding by the “click” reaction. • The influence of the functionalization scheme on surface coverage was investigated. - Abstract: This work presents an approach for producing a high-coverage single monolayer of magnetic nanoparticles using “click chemistry” between complementarily functionalized nanoparticles and a flat substrate. This method highlights essential aspects of the functionalization scheme for substrate surface and nanoparticles to produce exceptionally high surface coverage without sacrificing selectivity or control over the layer produced. The deposition of one single layer of magnetic particles without agglomeration, over a large area, with a nearly 100% coverage is confirmed by electron microscopy. Spectroscopic techniques, supplemented by computational predictions, are used to interrogate the chemistry of the attachment and to confirm covalent binding, rather than attachment through self-assembly or weak van der Waals bonding. Density functional theory calculations for the surface intermediate of this copper-catalyzed process provide mechanistic insight into the effects of the functionalization scheme on surface coverage. Based on this analysis, it appears that steric limitations of the intermediate structure affect nanoparticle coverage on a flat solid substrate; however, this can be overcome by designing a functionalization scheme in such a way that the copper-based intermediate is formed on the spherical nanoparticles instead. This observation can be carried over to other approaches for creating highly controlled single- or multilayered nanostructures of a wide range of materials to result in high coverage and possibly, conformal filling.

  14. A Universe without Weak Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Harnik, Roni; Kribs, Graham D.; Perez, Gilad

    2006-04-07

    A universe without weak interactions is constructed that undergoes big-bang nucleosynthesis, matter domination, structure formation, and star formation. The stars in this universe are able to burn for billions of years, synthesize elements up to iron, and undergo supernova explosions, dispersing heavy elements into the interstellar medium. These definitive claims are supported by a detailed analysis where this hypothetical ''Weakless Universe'' is matched to our Universe by simultaneously adjusting Standard Model and cosmological parameters. For instance, chemistry and nuclear physics are essentially unchanged. The apparent habitability of the Weakless Universe suggests that the anthropic principle does not determine the scale of electroweak breaking, or even require that it be smaller than the Planck scale, so long as technically natural parameters may be suitably adjusted. Whether the multi-parameter adjustment is realized or probable is dependent on the ultraviolet completion, such as the string landscape. Considering a similar analysis for the cosmological constant, however, we argue that no adjustments of other parameters are able to allow the cosmological constant to raise up even remotely close to the Planck scale while obtaining macroscopic structure. The fine-tuning problems associated with the electroweak breaking scale and the cosmological constant therefore appear to be qualitatively different from the perspective of obtaining a habitable universe.

  15. From strong to weak coupling in holographic models of thermalization

    Energy Technology Data Exchange (ETDEWEB)

    Grozdanov, Sašo; Kaplis, Nikolaos [Instituut-Lorentz for Theoretical Physics, Leiden University,Niels Bohrweg 2, Leiden 2333 CA (Netherlands); Starinets, Andrei O. [Rudolf Peierls Centre for Theoretical Physics, University of Oxford,1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2016-07-29

    We investigate the analytic structure of thermal energy-momentum tensor correlators at large but finite coupling in quantum field theories with gravity duals. We compute corrections to the quasinormal spectra of black branes due to the presence of higher derivative R{sup 2} and R{sup 4} terms in the action, focusing on the dual to N=4 SYM theory and Gauss-Bonnet gravity. We observe the appearance of new poles in the complex frequency plane at finite coupling. The new poles interfere with hydrodynamic poles of the correlators leading to the breakdown of hydrodynamic description at a coupling-dependent critical value of the wave-vector. The dependence of the critical wave vector on the coupling implies that the range of validity of the hydrodynamic description increases monotonically with the coupling. The behavior of the quasinormal spectrum at large but finite coupling may be contrasted with the known properties of the hierarchy of relaxation times determined by the spectrum of a linearized kinetic operator at weak coupling. We find that the ratio of a transport coefficient such as viscosity to the relaxation time determined by the fundamental non-hydrodynamic quasinormal frequency changes rapidly in the vicinity of infinite coupling but flattens out for weaker coupling, suggesting an extrapolation from strong coupling to the kinetic theory result. We note that the behavior of the quasinormal spectrum is qualitatively different depending on whether the ratio of shear viscosity to entropy density is greater or less than the universal, infinite coupling value of ℏ/4πk{sub B}. In the former case, the density of poles increases, indicating a formation of branch cuts in the weak coupling limit, and the spectral function shows the appearance of narrow peaks. We also discuss the relation of the viscosity-entropy ratio to conjectured bounds on relaxation time in quantum systems.

  16. Bounds for Asian basket options

    Science.gov (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle

    2008-09-01

    In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.

  17. Weak-Values Metrological Techniques for Parameter Estimation

    Science.gov (United States)

    Martinez-Rincon, Julian Rodrigo

    Precision measurements are bounded by the Standard Quantum Limit, and preparing non-classical states is often used to circumvent such a limit. In all cases, it is common to improve the precision in a parameter estimation procedure by averaging measurements of a large ensemble of identically prepared systems. However, such a task cannot be performed indefinitely due to sources of technical noise setting an experimental bound. Weak-Value Amplification (WVA) allows one to overcome some of these issues by amplifying a signal of interest above the technical-noise floor. This built-in robustness to external sources of noise relies on a weak coupling to a meter and postselection. In this document we evaluate, theoretically and experimentally, under what circumstances the technique is superior to non-postselected standard techniques. We also present a novel protocol where a WVA-like response is induced in an optical homodyne-type detection technique. We dub this technique Almost-Balanced Weak Values (ABWV) and present three experimental measurements of different physical velocities to evaluate the practical advantages over the well-known technique of WVA. In addition, we point out the existence of a third postselected-weak-measurements technique for metrology, Inverse Weak Value (IWV), that has been ignored by the scientific community. We use this protocol to measure ultra small tilts of a mirror in a Sagnac interferometer. We report all three techniques as complementary to each other, and show their robustness for low-frequency signals.

  18. Weak Measurement and Quantum Correlation

    Indian Academy of Sciences (India)

    Arun Kumar Pati

    The concept of the weak measurements, for the first time, was introduced by Aharonov et al.1. Quantum state is preselected in |ψi〉 and allowed to interact weakly with apparatus. Measurement strength can be tuned and for “small g(t)” it is called 'weak measurement'. With postselection in |ψf 〉, apparatus state is shifted by an ...

  19. A Weak Comparison Principle for Reaction-Diffusion Systems

    Directory of Open Access Journals (Sweden)

    José Valero

    2012-01-01

    Full Text Available We prove a weak comparison principle for a reaction-diffusion system without uniqueness of solutions. We apply the abstract results to the Lotka-Volterra system with diffusion, a generalized logistic equation, and to a model of fractional-order chemical autocatalysis with decay. Moreover, in the case of the Lotka-Volterra system a weak maximum principle is given, and a suitable estimate in the space of essentially bounded functions L∞ is proved for at least one solution of the problem.

  20. Hadron-nucleus bound states

    CERN Document Server

    Yamazaki, T

    2000-01-01

    A new type of nuclear spectroscopy to study hadron-nucleus bound states is described. The first successful experiment was to search for deeply bound pi sup - states in heavy nuclei using the sup 2 sup 0 sup 8 Pb(d, sup 3 He) reaction at GSI, in which a narrow peak arising from the 2p pi sup - orbital coupled with the neutron-hole states was observed at 135 MeV excitation energy. An improved experiment has just been carried out to separately identify the 1s and 2p pi sup - states. These experiments provide important information on the local potential strength, from which the effective mass of pi sup - is deduced to be 20 MeV. This method will be extended to search for eta and omega bound states as well as for K sup - bound states. The advantage of the bound-state spectroscopy versus invariant mass spectroscopy is emphasized.

  1. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long...

  2. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    2010-01-01

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and longterm...

  3. Shape Selection of Surface-Bound Helical Filaments: Biopolymers on Curved Membranes.

    Science.gov (United States)

    Quint, David A; Gopinathan, Ajay; Grason, Gregory M

    2016-10-04

    Motivated to understand the behavior of biological filaments interacting with membranes of various types, we employ a theoretical model for the shape and thermodynamics of intrinsically helical filaments bound to curved membranes. We show that filament-surface interactions lead to a host of nonuniform shape equilibria, in which filaments progressively unwind from their native twist with increasing surface interaction and surface curvature, ultimately adopting uniform-contact curved shapes. The latter effect is due to nonlinear coupling between elastic twist and bending of filaments on anisotropically curved surfaces such as the cylindrical surfaces considered here. Via a combination of numerical solutions and asymptotic analysis of shape equilibria, we show that filament conformations are critically sensitive to the surface curvature in both the strong- and weak-binding limits. These results suggest that local structure of membrane-bound chiral filaments is generically sensitive to the curvature radius of the surface to which it is bound, even when that radius is much larger than the filament's intrinsic pitch. Typical values of elastic parameters and interaction energies for several prokaryotic and eukaryotic filaments indicate that biopolymers are inherently very sensitive to the coupling between twist, interactions, and geometry and that this could be exploited for regulation of a variety of processes such as the targeted exertion of forces, signaling, and self-assembly in response to geometric cues including the local mean and Gaussian curvatures. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Viscous dispersion effects on bound-state formation in falling liquid films

    Science.gov (United States)

    Pradas, Marc; Tseluiko, Dmitri; Kalliadasis, Serafim

    2010-11-01

    We examine the influence of viscous dispersion on the interaction of two-dimensional solitary pulses in falling liquid films at moderate Reynolds number. We make use of an averaged model that includes second-order viscous effects in the long-wave expansion. These effects play a dispersive role affecting primarily the shape of the capillary ripples in front of the solitary pulses. We show that different physical parameters, such as surface tension and viscosity, play a crucial role in the interaction between pulses giving rise eventually to the formation of bound states consisting of two or more pulses separated by well-defined distances and travelling at the same velocity. By developing a coherent-structures theory that assumes weak interaction between the pulses, we are able to theoretically predict the pulse-separation distances for which bound states are formed. It is shown that viscous dispersion significantly affects the distances at which bound states are observed. In all cases, there is very good agreement between the theory and computations of the fully nonlinear system.

  5. Weapon of the Weak?

    DEFF Research Database (Denmark)

    Amber, Van der Graaf; Otjes, Simon; Rasmussen, Anne

    2016-01-01

    on the sparse existing literature on interest groups and social media in a quantitative, structural analysis of both the range and volume of social media use examining a data set of groups active in European Union lobbying. Despite the positive expectations, we find limited evidence that social media have been...... if they lose ground to traditional membership groups when the actual volume of Twitter and Facebook use is assessed....

  6. Weak-value Metrology and Shot-Noise Limited Measurements

    Science.gov (United States)

    Viza, Gerardo Ivan

    This thesis contains a subset of the research in which I have participated in during my studies at the University of Rochester. It contains three projects and one overarching theme of weak-value metrology. We start with chapter 1 where we cover the historical background leading up to quantum optics, which we use for precision metrology. We also introduce the weak-value formulation and give examples of metrological implementations for parameter estimation. Chapter 2 introduces two experiments to measure a longitudinal velocity and a transverse momentum kick. We show that weak-value based techniques are shot-noise limited because we saturate the Cramer-Rao bound for the estimator used, and efficient because we experimentally demonstrate there is virtually no loss of Fisher information of the parameter of interest from the discarded events. In Chapter 3 we present a comparison of two experiments that measure a beam deflection. One experiment is a weak-value based technique, while the other is the standard focusing technique. We set up the two experiments in the presence of simulated technical noise sources and show how the weak-value based technique out performs the standard technique in both visibility and in deviation of the transverse momentum kick. Chapter 4 contains work of the exploration of concatenated postselection for weak-value amplification. We demonstrate an optimization and conditions where postselecting on two degrees of freedom can be beneficial to enhance the weak-value amplification.

  7. Structures of the N-acetyltransferase domain of Xylella fastidiosa N-acetyl-L-glutamate synthase/kinase with and without a His tag bound to N-acetyl-L-glutamate.

    Science.gov (United States)

    Zhao, Gengxiang; Jin, Zhongmin; Allewell, Norma M; Tuchman, Mendel; Shi, Dashuang

    2015-01-01

    Structures of the catalytic N-acetyltransferase (NAT) domain of the bifunctional N-acetyl-L-glutamate synthase/kinase (NAGS/K) from Xylella fastidiosa bound to N-acetyl-L-glutamate (NAG) with and without an N-terminal His tag have been solved and refined at 1.7 and 1.4 Å resolution, respectively. The NAT domain with an N-terminal His tag crystallized in space group P4(1)2(1)2, with unit-cell parameters a=b=51.72, c=242.31 Å. Two subunits form a molecular dimer in the asymmetric unit, which contains ∼41% solvent. The NAT domain without an N-terminal His tag crystallized in space group P21, with unit-cell parameters a=63.48, b=122.34, c=75.88 Å, β=107.6°. Eight subunits, which form four molecular dimers, were identified in the asymmetric unit, which contains ∼38% solvent. The structures with and without the N-terminal His tag provide an opportunity to evaluate how the His tag affects structure and function. Furthermore, multiple subunits in different packing environments allow an assessment of the plasticity of the NAG binding site, which might be relevant to substrate binding and product release. The dimeric structure of the X. fastidiosa N-acetytransferase (xfNAT) domain is very similar to that of human N-acetyltransferase (hNAT), reinforcing the notion that mammalian NAGS is evolutionally derived from bifunctional bacterial NAGS/K.

  8. Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site.

    Science.gov (United States)

    Harel, Michal; Sonoda, Leilani K; Silman, Israel; Sussman, Joel L; Rosenberry, Terrone L

    2008-06-25

    Acetylcholinesterase plays a key role in cholinergic synaptic transmission by hydrolyzing the neurotransmitter acetylcholine with one of the highest known catalytic rate constants. Hydrolysis occurs in a narrow and deep gorge that contains two sites of ligand binding: A peripheral site, or P-site, near the gorge entrance that contributes to catalytic efficiency both by transiently trapping substrate molecules as they enter the gorge and by allosterically accelerating the transfer of the substrate acyl group to a serine hydroxyl in an acylation site or A-site at the base of the gorge. Thioflavin T is a useful reporter of ligand interactions with the A-site. It binds specifically to the P-site with fluorescence that is enhanced approximately 1000-fold over that of unbound thioflavin T, and the enhanced fluorescence is quenched 1.5- to 4-fold when another ligand binds to the A-site in a ternary complex. To clarify the structural basis of this advantageous signal change, we here report the X-ray structure of the complex of thioflavin T with Torpedo californica acetylcholinesterase. The two aromatic rings in thioflavin T are coplanar and are packed snugly parallel to the aromatic side chains of Trp279, Tyr334, and Phe330. Overlays of this structure with the crystal structures of Torpedo californica acetylcholinesterase complexes with either edrophonium or m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, two small aromatic ligands that bind specifically to the A-site, indicate that the phenyl side chain of Phe330 must rotate to sterically accommodate both thioflavin T and the A-site ligand in the ternary complex. This rotation may allow some relaxation of the strict coplanarity of the aromatic rings in the bound thioflavin T and result in partial quenching of its fluorescence.

  9. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

    Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H

    2007-03-20

    Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic

  10. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

    Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.

  11. Computational Lower Bounds Using Diagonalization

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 7. Computational Lower Bounds Using Diagonalization - Languages, Turing Machines and Complexity Classes. M V Panduranga Rao. General Article Volume 14 Issue 7 July 2009 pp 682-690 ...

  12. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg

    2014-01-01

    perspective may affect the commonly employed explanatory factors of administrative capacities, misfit and the heterogeneity of preferences among veto players. To prevent retrospective rationalisation of the transposition process, this paper traces this process as it unfolded in Denmark and the Netherlands....... As bounded rationality is apparent in the transposition processes in these relatively well-organised countries, future transposition studies should devote greater consideration to the bounded rationality perspective....

  13. Resisting Weakness of the Will.

    Science.gov (United States)

    Levy, Neil

    2011-01-01

    I develop an account of weakness of the will that is driven by experimental evidence from cognitive and social psychology. I will argue that this account demonstrates that there is no such thing as weakness of the will: no psychological kind corresponds to it. Instead, weakness of the will ought to be understood as depletion of System II resources. Neither the explanatory purposes of psychology nor our practical purposes as agents are well-served by retaining the concept. I therefore suggest that we ought to jettison it, in favour of the vocabulary and concepts of cognitive psychology.

  14. Limits on the electromagnetic and weak dipole moments of the tau-lepton in a 331 model

    Energy Technology Data Exchange (ETDEWEB)

    Gutiérrez-Rodríguez, A. [Facultad de Física, Universidad Autónoma de Zacatecas Apartado, Postal C-580, 98060 Zacatecas, México (Mexico); Hernández-Ruíz, M.A. [Facultad de Ciencias Químicas, Universidad Autónoma de Zacatecas Apartado, Postal 585, 98060 Zacatecas, México (Mexico); Castañeda-Almanza, C.P.; Espinoza-Garrido, A.; Chubykalo, A. [Facultad de Física, Universidad Autónoma de Zacatecas Apartado, Postal C-580, 98060 Zacatecas, México (Mexico)

    2014-08-15

    Using as an input the data obtained by the L3 and OPAL Collaborations for the reaction e{sup +}e{sup −}→τ{sup +}τ{sup −}γ at the Z{sub 1}-pole, we obtained bounds on the electromagnetic and weak dipole moments of the tau-lepton in the context of a 331 model. Our bounds on the electromagnetic moments are consistent with the bounds obtained by the L3 and OPAL Collaborations for the reaction e{sup +}e{sup −}→τ{sup +}τ{sup −}γ. We also obtained bounds on the tau weak dipole moments which are consistent with the bounds obtained recently by the DELPHI, ALEPH and BELLE Collaborations from the reaction e{sup +}e{sup −}→τ{sup +}τ{sup −}. Our work complements other studies on the electromagnetic and weak dipole moments of the tau-lepton.

  15. Limits on the electromagnetic and weak dipole moments of the tau-lepton in a 331 model

    Science.gov (United States)

    Gutiérrez-Rodríguez, A.; Hernández-Ruíz, M. A.; Castañeda-Almanza, C. P.; Espinoza-Garrido, A.; Chubykalo, A.

    2014-08-01

    Using as an input the data obtained by the L3 and OPAL Collaborations for the reaction e+e- →τ+τ- γ at the Z1-pole, we obtained bounds on the electromagnetic and weak dipole moments of the tau-lepton in the context of a 331 model. Our bounds on the electromagnetic moments are consistent with the bounds obtained by the L3 and OPAL Collaborations for the reaction e+e- →τ+τ- γ. We also obtained bounds on the tau weak dipole moments which are consistent with the bounds obtained recently by the DELPHI, ALEPH and BELLE Collaborations from the reaction e+e- →τ+τ-. Our work complements other studies on the electromagnetic and weak dipole moments of the tau-lepton.

  16. Dynamic properties of superconducting weak links

    Science.gov (United States)

    Schmid, Albert; Schön, Gerd; Tinkham, Michael

    1980-06-01

    A comprehensive theoretical picture of the dynamic properties of the order parameter and the quasiparticles in superconducting short weak links is presented. Both diffusion and inelastic scattering are found to be important in relaxing nonequilibrium populations. At low voltages a dissipative current, which is considerably larger than the normal ohmic current, is found and at higher voltages the maximum supercurrent is enhanced. These effects describe quantitatively well the foot structure in the I-V characteristic observed experimentally by Octavio, Skocpol, and Tinkham.

  17. Spectral singularities and zero energy bound states

    Energy Technology Data Exchange (ETDEWEB)

    Heiss, W.D. [National Institute for Theoretical Physics, Stellenbosch Institute for Advanced Study, and Institute of Theoretical Physics, University of Stellenbosch, 7602 Matieland (South Africa); Nazmitdinov, R.G. [Department de Fisica, Universitat de les Illes Balears, E-07122 Palma de Mallorca (Spain); Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation)

    2011-08-15

    Single particle scattering around zero energy is re-analysed in view of recent experiments with ultra-cold atoms, nano-structures and nuclei far from the stability valley. For non-zero orbital angular momentum the low energy scattering cross section exhibits dramatic changes depending on the occurrence of either a near resonance or a bound state or the situation in between, that is a bound state at zero energy. Such state is singular in that it has an infinite scattering length, behaves for the eigenvalues but not for the eigenfunctions as an exceptional point and has no pole in the scattering function. These results should be observable whenever the interaction or scattering length can be controlled. (authors)

  18. Weak Coupling Phases future directions

    CERN Document Server

    Rosner, Jonathan L.

    2003-01-01

    Recent results obtained from B decays on the phases of weak couplings described by the Cabibbo-Kobayashi-Maskawa (CKM) matrix are discussed, with particular emphasis on $\\alpha$ and $\\gamma = \\pi - \\beta - \\alpha$.

  19. Weakly compact operators and interpolation

    OpenAIRE

    Maligranda, Lech

    1992-01-01

    The class of weakly compact operators is, as well as the class of compact operators, a fundamental operator ideal. They were investigated strongly in the last twenty years. In this survey, we have collected and ordered some of this (partly very new) knowledge. We have also included some comments, remarks and examples. The class of weakly compact operators is, as well as the class of compact operators, a fundamental operator ideal. They were investigated strongly in the last twenty years. I...

  20. Weak interactions of elementary particles

    CERN Document Server

    Okun, Lev Borisovich

    1965-01-01

    International Series of Monographs in Natural Philosophy, Volume 5: Weak Interaction of Elementary Particles focuses on the composition, properties, and reactions of elementary particles and high energies. The book first discusses elementary particles. Concerns include isotopic invariance in the Sakata model; conservation of fundamental particles; scheme of isomultiplets in the Sakata model; universal, unitary-symmetric strong interaction; and universal weak interaction. The text also focuses on spinors, amplitudes, and currents. Wave function, calculation of traces, five bilinear covariants,

  1. Acute muscular weakness in children

    Directory of Open Access Journals (Sweden)

    Ricardo Pablo Javier Erazo Torricelli

    Full Text Available ABSTRACT Acute muscle weakness in children is a pediatric emergency. During the diagnostic approach, it is crucial to obtain a detailed case history, including: onset of weakness, history of associated febrile states, ingestion of toxic substances/toxins, immunizations, and family history. Neurological examination must be meticulous as well. In this review, we describe the most common diseases related to acute muscle weakness, grouped into the site of origin (from the upper motor neuron to the motor unit. Early detection of hyperCKemia may lead to a myositis diagnosis, and hypokalemia points to the diagnosis of periodic paralysis. Ophthalmoparesis, ptosis and bulbar signs are suggestive of myasthenia gravis or botulism. Distal weakness and hyporeflexia are clinical features of Guillain-Barré syndrome, the most frequent cause of acute muscle weakness. If all studies are normal, a psychogenic cause should be considered. Finding the etiology of acute muscle weakness is essential to execute treatment in a timely manner, improving the prognosis of affected children.

  2. Precision metrology using weak measurements.

    Science.gov (United States)

    Zhang, Lijian; Datta, Animesh; Walmsley, Ian A

    2015-05-29

    Weak values and measurements have been proposed as a means to achieve dramatic enhancements in metrology based on the greatly increased range of possible measurement outcomes. Unfortunately, the very large values of measurement outcomes occur with highly suppressed probabilities. This raises three vital questions in weak-measurement-based metrology. Namely, (Q1) Does postselection enhance the measurement precision? (Q2) Does weak measurement offer better precision than strong measurement? (Q3) Is it possible to beat the standard quantum limit or to achieve the Heisenberg limit with weak measurement using only classical resources? We analyze these questions for two prototypical, and generic, measurement protocols and show that while the answers to the first two questions are negative for both protocols, the answer to the last is affirmative for measurements with phase-space interactions, and negative for configuration space interactions. Our results, particularly the ability of weak measurements to perform at par with strong measurements in some cases, are instructive for the design of weak-measurement-based protocols for quantum metrology.

  3. Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis

    Science.gov (United States)

    Zúñiga, Matías A.; Alderete, Joel B.; Jaña, Gonzalo A.; Jiménez, Verónica A.

    2017-07-01

    Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU-tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA-tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug-tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.

  4. On the molecular basis of the recognition of angiotensin II (AII) : NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131

    NARCIS (Netherlands)

    Tzakos, A.G.; Bonvin, A.M.J.J.; Troganis, A.; Cordopatis, P.; Amzel, M.L.; Gerothanassis, I.P.; van Nuland, N.A.J.

    2003-01-01

    The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints. After final refinement in explicit water, a family of 13 structures was obtained with a backbone

  5. Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure

    Directory of Open Access Journals (Sweden)

    Park Jaeok

    2012-12-01

    absence of bound IPP. Q242 plays the role of a gatekeeper and directly controls the anchoring of R351 side chain. The interactions between the residues K57 and N59 and those upstream and downstream of Y349 are likely responsible for the switch activation. The findings of this study can be exploited for structure-guided optimization of existing inhibitors as well as development of new pharmacophores.

  6. On the molecular basis of the recognition of angiotensin II (AII) : NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131

    National Research Council Canada - National Science Library

    Tzakos, A.G; Bonvin, A.M.J.J; Troganis, A; Cordopatis, P; Amzel, M.L; Gerothanassis, I.P; van Nuland, N.A.J

    2003-01-01

    The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints...

  7. Space-bounded communication complexity

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Chen, Shiteng; Papakonstantinou, Periklis A.

    2013-01-01

    -obliviousness shows up. For this model we also introduce new techniques through which certain limitations of space-bounded computation are revealed. One of the main motivations of this work is in understanding the difference in the use of space when computing the following functions: Equality (EQ), Inner Product (IP......In the past thirty years, Communication Complexity has emerged as a foundational tool to proving lower bounds in many areas of computer science. Its power comes from its generality, but this generality comes at a price---no superlinear communication lower bound is possible, since a player may...... communicate his entire input. However, what if the players are limited in their ability to recall parts of their interaction? We introduce memory models for 2-party communication complexity. Our general model is as follows: two computationally unrestricted players, Alice and Bob, each have s(n) bits of memory...

  8. Aerodynamics of intermittent bounds in flying birds

    Science.gov (United States)

    Tobalske, Bret W.; Hearn, Jason W. D.; Warrick, Douglas R.

    Flap-bounding is a common flight style in small birds in which flapping phases alternate with flexed-wing bounds. Body lift is predicted to be essential to making this flight style an aerodynamically attractive flight strategy. To elucidate the contributions of the body and tail to lift and drag during the flexed-wing bound phase, we used particle image velocimetry (PIV) and measured properties of the wake of zebra finch (Taeniopygia guttata, N = 5), flying at 6-10 m s- 1 in a variable speed wind tunnel as well as flow around taxidermically prepared specimens (N = 4) mounted on a sting instrumented with force transducers. For the specimens, we varied air velocity from 2 to 12 m s- 1 and body angle from -15∘ to 50∘. The wake of bounding birds and mounted specimens consisted of a pair of counterrotating vortices shed into the wake from the tail, with induced downwash in the sagittal plane and upwash in parasagittal planes lateral to the bird. This wake structure was present even when the tail was entirely removed. We observed good agreement between force measures derived from PIV and force transducers over the range of body angles typically used by zebra finch during forward flight. Body lift:drag (L:D) ratios averaged 1.4 in live birds and varied between 1 and 1.5 in specimens at body angles from 10∘ to 30∘. Peak (L:D) ratio was the same in live birds and specimens (1.5) and was exhibited in specimens at body angles of 15∘ or 20∘, consistent with the lower end of body angles utilized during bounds. Increasing flight velocity in live birds caused a decrease in CL and CD from maximum values of 1.19 and 0.95 during flight at 6 m s- 1 to minimum values of 0.70 and 0.54 during flight at 10 m s- 1. Consistent with delta-wing theory as applied to birds with a graduated-tail shape, trimming the tail to 0 and 50% of normal length reduced L:D ratios and extending tail length to 150% of normal increased L:D ratio. As downward induced velocity is present in the

  9. Modeling Chemical Interaction Profiles: II. Molecular Docking, Spectral Data-Activity Relationship, and Structure-Activity Relationship Models for Potent and Weak Inhibitors of Cytochrome P450 CYP3A4 Isozyme

    Directory of Open Access Journals (Sweden)

    Eugene Demchuk

    2012-03-01

    Full Text Available Polypharmacy increasingly has become a topic of public health concern, particularly as the U.S. population ages. Drug labels often contain insufficient information to enable the clinician to safely use multiple drugs. Because many of the drugs are bio-transformed by cytochrome P450 (CYP enzymes, inhibition of CYP activity has long been associated with potentially adverse health effects. In an attempt to reduce the uncertainty pertaining to CYP-mediated drug-drug/chemical interactions, an interagency collaborative group developed a consensus approach to prioritizing information concerning CYP inhibition. The consensus involved computational molecular docking, spectral data-activity relationship (SDAR, and structure-activity relationship (SAR models that addressed the clinical potency of CYP inhibition. The models were built upon chemicals that were categorized as either potent or weak inhibitors of the CYP3A4 isozyme. The categorization was carried out using information from clinical trials because currently available in vitro high-throughput screening data were not fully representative of the in vivo potency of inhibition. During categorization it was found that compounds, which break the Lipinski rule of five by molecular weight, were about twice more likely to be inhibitors of CYP3A4 compared to those, which obey the rule. Similarly, among inhibitors that break the rule, potent inhibitors were 2–3 times more frequent. The molecular docking classification relied on logistic regression, by which the docking scores from different docking algorithms, CYP3A4 three-dimensional structures, and binding sites on them were combined in a unified probabilistic model. The SDAR models employed a multiple linear regression approach applied to binned 1D 13C-NMR and 1D 15N-NMR spectral descriptors. Structure-based and physical-chemical descriptors were used as the basis for developing SAR models by the decision forest method. Thirty-three potent inhibitors

  10. Quantum discord with weak measurements

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Uttam, E-mail: uttamsingh@hri.res.in; Pati, Arun Kumar, E-mail: akpati@hri.res.in

    2014-04-15

    Weak measurements cause small change to quantum states, thereby opening up the possibility of new ways of manipulating and controlling quantum systems. We ask, can weak measurements reveal more quantum correlation in a composite quantum state? We prove that the weak measurement induced quantum discord, called as the “super quantum discord”, is always larger than the quantum discord captured by the strong measurement. Moreover, we prove the monotonicity of the super quantum discord as a function of the measurement strength and in the limit of strong projective measurement the super quantum discord becomes the normal quantum discord. We find that unlike the normal discord, for pure entangled states, the super quantum discord can exceed the quantum entanglement. Our results provide new insights on the nature of quantum correlation and suggest that the notion of quantum correlation is not only observer dependent but also depends on how weakly one perturbs the composite system. We illustrate the key results for pure as well as mixed entangled states. -- Highlights: •Introduced the role of weak measurements in quantifying quantum correlation. •We have introduced the notion of the super quantum discord (SQD). •For pure entangled state, we show that the SQD exceeds the entanglement entropy. •This shows that quantum correlation depends not only on observer but also on measurement strength.

  11. Francium Spectroscopy for Weak Interaction Studies

    Science.gov (United States)

    Orozco, Luis

    2014-05-01

    Francium, a radioactive element, is the heaviest alkali. Its atomic and nuclear structure makes it an ideal laboratory to study the weak interaction. Laser trapping and cooling in-line with the superconducting LINAC accelerator at Stony Brook opened the precision study of its atomic structure. I will present our proposal and progress towards weak interaction measurements at TRIUMF, the National Canadian Accelerator in Vancouver. These include the commissioning run of the Francium Trapping Facility, hyperfine anomaly measurements on a chain of Fr isotopes, the nuclear anapole moment through parity non-conserving transitions in the ground state hyperfine manifold. These measurements should shed light on the nucleon-nucleon weak interaction. This work is done by the FrPNC collaboration: S. Aubin College of William and Mary, J. A. Behr TRIUMF, R. Collister U. Manitoba, E. Gomez UASLP, G. Gwinner U. Manitoba, M. R. Pearson TRIUMF, L. A. Orozco UMD, M. Tandecki TRIUMF, J. Zhang UMD Supported by NSF and DOE from the USA; TRIUMF, NRC and NSERC from Canada; and CONACYT from Mexico

  12. Weak-type (1,1 bounds for a class of operators with discrete kernel

    Directory of Open Access Journals (Sweden)

    Duván Cardona

    2015-01-01

    Full Text Available En este trabajo se investigará el tipo débil (1,1 de una cier ta clase de operadores con núcleo definido sobre Z × Z . Se estudiará la continuidad débil de operadores que son análogos discretos de los ahora c onocidos, oper- adores singulares integrales de Calderón-Zygmund. Los ope radores considera- dos surgen desde el estudio de operadores pseudo diferencia les de tipo discreto y versiones discretas de integrales singulares.

  13. Suppression of the weakly-bound excited Υ states in HI collisions

    CERN Multimedia

    2011-01-01

      CMS was able to observe for the first time this phenomenon by comparing last year’s HI collisions at 2.76 TeV/nucleon with the pp collisions that took place at the same energy earlier this year. For more, visit: http://bit.ly/Y-melting  

  14. Lifting a weak Poisson bracket to the algebra of forms

    Science.gov (United States)

    Lyakhovich, S.; Peddie, M.; Sharapov, A.

    2017-06-01

    We detail the construction of a weak Poisson bracket over a submanifold Σ of a smooth manifold M with respect to a local foliation of this submanifold. Such a bracket satisfies a weak type Jacobi identity but may be viewed as a usual Poisson bracket on the space of leaves of the foliation. We then lift this weak Poisson bracket to a weak odd Poisson bracket on the odd tangent bundle ΠTM, interpreted as a weak Koszul bracket on differential forms on M. This lift is achieved by encoding the weak Poisson structure into a homotopy Poisson structure on an extended manifold, and lifting the Hamiltonian function that generates this structure. Such a construction has direct physical interpretation. For a generic gauge system, the submanifold Σ may be viewed as a stationary surface or a constraint surface, with the foliation given by the foliation of the gauge orbits. Through this interpretation, the lift of the weak Poisson structure is simply a lift of the action generating the corresponding BRST operator of the system.

  15. Warping the Weak Gravity Conjecture

    Directory of Open Access Journals (Sweden)

    Karta Kooner

    2016-08-01

    Full Text Available The Weak Gravity Conjecture, if valid, rules out simple models of Natural Inflation by restricting their axion decay constant to be sub-Planckian. We revisit stringy attempts to realise Natural Inflation, with a single open string axionic inflaton from a probe D-brane in a warped throat. We show that warped geometries can allow the requisite super-Planckian axion decay constant to be achieved, within the supergravity approximation and consistently with the Weak Gravity Conjecture. Preliminary estimates of the brane backreaction suggest that the probe approximation may be under control. However, there is a tension between large axion decay constant and high string scale, where the requisite high string scale is difficult to achieve in all attempts to realise large field inflation using perturbative string theory. We comment on the Generalized Weak Gravity Conjecture in the light of our results.

  16. Weak ferromagnetism and nanodimensional ferroelectric domain structure stabilized in the polar phase of Bi{sub 1−x}Nd{sub x}FeO{sub 3} multiferroics via Ti doping

    Energy Technology Data Exchange (ETDEWEB)

    Khomchenko, V. A., E-mail: uladzimir@fis.uc.pt; Paixão, J. A. [CEMDRX/Department of Physics, University of Coimbra, P-3004-516 Coimbra (Portugal); Pereira, L. C. J. [Unidade de Ciências Químicas e Radiofarmacêuticas, IST/CTN, Instituto Superior Técnico, Universidade Técnica de Lisboa/CFMCUL, P-2686-953 Sacavém (Portugal)

    2014-04-28

    Crystal structure, microstructure, local ferroelectric, and magnetic properties of the Bi{sub 0.9}Nd{sub 0.1}Fe{sub 1−x}Ti{sub x}O{sub 3} samples have been investigated at room temperature to reveal the effect of Ti{sup 4+} doping on the multiferroic behavior of the lanthanide-modified compound representing a polar (space group R3c) antiferromagnetic phase of the Bi{sub 1−x}Ln{sub x}FeO{sub 3} perovskites. Ti doping results in a gradual suppression of the rhombohedral distortions, however, symmetry of the crystal structure remains the same in the entire concentration range allowing the single-phase perovskites to be obtained (x ≤ 0.08). The doping tends to reduce existing lone-pair cation-driven polar displacements, thus giving rise to a decrease of the ferroelectric polarization in the Bi{sub 0.9}Nd{sub 0.1}Fe{sub 1−x}Ti{sub x}O{sub 3} (x→0.08) series. A drastic (from ∼10 μm for x = 0 to ∼1 μm for 0.02 ≤ x ≤ 0.08) decrease of the average grain size induced by the doping is accompanied by the formation of a ferroelectric domain structure with the average domain width of ∼40 nm. Finally, the doping was shown to induce an antiferromagnetic to weak ferromagnetic transformation. The maximum remanent magnetization observed in the Bi{sub 0.9}Nd{sub 0.1}Fe{sub 1−x}Ti{sub x}O{sub 3} series at x ∼ 0.05 coincides with the locked magnetization releasing upon the magnetic field-induced suppression of the magnetic cycloid in pure BiFeO{sub 3}.

  17. Nonlinear waves and weak turbulence

    CERN Document Server

    Zakharov, V E

    1997-01-01

    This book is a collection of papers on dynamical and statistical theory of nonlinear wave propagation in dispersive conservative media. Emphasis is on waves on the surface of an ideal fluid and on Rossby waves in the atmosphere. Although the book deals mainly with weakly nonlinear waves, it is more than simply a description of standard perturbation techniques. The goal is to show that the theory of weakly interacting waves is naturally related to such areas of mathematics as Diophantine equations, differential geometry of waves, Poincaré normal forms, and the inverse scattering method.

  18. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.

    2009-01-01

    This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...

  19. Distance bounds on quantum dynamics

    Science.gov (United States)

    Lidar, Daniel A.; Zanardi, Paolo; Khodjasteh, Kaveh

    2008-07-01

    We derive rigorous upper bounds on the distance between quantum states in an open-system setting in terms of the operator norm between Hamiltonians describing their evolution. We illustrate our results with an example taken from protection against decoherence using dynamical decoupling.

  20. Moderate deviations for bounded subsequences

    Directory of Open Access Journals (Sweden)

    George Stoica

    2006-01-01

    Full Text Available We study Davis' series of moderate deviations probabilities for Lp-bounded sequences of random variables (p>2. A certain subseries therein is convergent for the same range of parameters as in the case of martingale difference or i.i.d. sequences.

  1. The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors.

    Science.gov (United States)

    Townsend, Philip D; Jungwirth, Britta; Pojer, Florence; Bußmann, Michael; Money, Victoria A; Cole, Stewart T; Pühler, Alfred; Tauch, Andreas; Bott, Michael; Cann, Martin J; Pohl, Ehmke

    2014-01-01

    The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition.

  2. The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors.

    Directory of Open Access Journals (Sweden)

    Philip D Townsend

    Full Text Available The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition.

  3. Submanifolds weakly associated with graphs

    Indian Academy of Sciences (India)

    Sci. (Math. Sci.) Vol. 119, No. 3, June 2009, pp. 297–318. © Printed in India. Submanifolds weakly associated with graphs. A CARRIAZO, L M FERN ´ANDEZ and A RODRÍGUEZ-HIDALGO. Department of Geometry and Topology, Faculty of Mathematics, University of Sevilla,. Apartado de Correos 1160, 41080-Sevilla, Spain.

  4. Beam splitting on weak illumination.

    Science.gov (United States)

    Snyder, A W; Buryak, A V; Mitchell, D J

    1998-01-01

    We demonstrate, in both two and three dimensions, how a self-guided beam in a non-Kerr medium is split into two beams on weak illumination. We also provide an elegant physical explanation that predicts the universal character of the observed phenomenon. Possible applications of our findings to guiding light with light are also discussed.

  5. On Weak-BCC-Algebras

    Science.gov (United States)

    Thomys, Janus; Zhang, Xiaohong

    2013-01-01

    We describe weak-BCC-algebras (also called BZ-algebras) in which the condition (x∗y)∗z = (x∗z)∗y is satisfied only in the case when elements x, y belong to the same branch. We also characterize ideals, nilradicals, and nilpotent elements of such algebras. PMID:24311983

  6. Voltage Weak DC Distribution Grids

    NARCIS (Netherlands)

    Hailu, T.G.; Mackay, L.J.; Ramirez Elizondo, L.M.; Ferreira, J.A.

    2017-01-01

    This paper describes the behavior of voltage weak DC distribution systems. These systems have relatively small system capacitance. The size of system capacitance, which stores energy, has a considerable effect on the value of fault currents, control complexity, and system reliability. A number of

  7. Weak solutions for nonlocal evolution variational inequalities involving gradient constraints and variable exponent

    Directory of Open Access Journals (Sweden)

    Mingqi Xiang

    2013-04-01

    Full Text Available In this article, we study a class of nonlocal quasilinear parabolic variational inequality involving $p(x$-Laplacian operator and gradient constraint on a bounded domain. Choosing a special penalty functional according to the gradient constraint, we transform the variational inequality to a parabolic equation. By means of Galerkin's approximation method, we obtain the existence of weak solutions for this equation, and then through a priori estimates, we obtain the weak solutions of variational inequality.

  8. Fast concurrent array-based stacks, queues and deques using fetch-and-increment-bounded, fetch-and-decrement-bounded and store-on-twin synchronization primitives

    Science.gov (United States)

    Chen, Dong; Gara, Alana; Heidelberger, Philip; Kumar, Sameer; Ohmacht, Martin; Steinmacher-Burow, Burkhard; Wisniewski, Robert

    2014-09-16

    Implementation primitives for concurrent array-based stacks, queues, double-ended queues (deques) and wrapped deques are provided. In one aspect, each element of the stack, queue, deque or wrapped deque data structure has its own ticket lock, allowing multiple threads to concurrently use multiple elements of the data structure and thus achieving high performance. In another aspect, new synchronization primitives FetchAndIncrementBounded (Counter, Bound) and FetchAndDecrementBounded (Counter, Bound) are implemented. These primitives can be implemented in hardware and thus promise a very fast throughput for queues, stacks and double-ended queues.

  9. Competing weak localization and weak antilocalization in ultrathin topological insulators.

    Science.gov (United States)

    Lang, Murong; He, Liang; Kou, Xufeng; Upadhyaya, Pramey; Fan, Yabin; Chu, Hao; Jiang, Ying; Bardarson, Jens H; Jiang, Wanjun; Choi, Eun Sang; Wang, Yong; Yeh, Nai-Chang; Moore, Joel; Wang, Kang L

    2013-01-09

    We demonstrate evidence of a surface gap opening in topological insulator (TI) thin films of (Bi(0.57)Sb(0.43))(2)Te(3) below six quintuple layers through transport and scanning tunneling spectroscopy measurements. By effective tuning the Fermi level via gate-voltage control, we unveil a striking competition between weak localization and weak antilocalization at low magnetic fields in nonmagnetic ultrathin films, possibly owing to the change of the net Berry phase. Furthermore, when the Fermi level is swept into the surface gap of ultrathin samples, the overall unitary behaviors are revealed at higher magnetic fields, which are in contrast to the pure WAL signals obtained in thicker films. Our findings show an exotic phenomenon characterizing the gapped TI surface states and point to the future realization of quantum spin Hall effect and dissipationless TI-based applications.

  10. From superWIMPs to decaying dark matter. Models, bounds and indirect searches

    Energy Technology Data Exchange (ETDEWEB)

    Weniger, Christoph

    2010-06-15

    Despite lots of observational and theoretical efforts, the particle nature of dark matter remains unknown. Beyond the paradigmatic WIMPs (Weakly Interacting Massive Particles), many theoretically well motivated models exist where dark matter interacts much more weakly than electroweak with Standard Model particles. In this case new phenomena occur, like the decay of dark matter or the interference with the standard cosmology of the early Universe. In this thesis we study some of these aspects of superweakly coupled dark matter in general, and in the special case of hidden U(1){sub X} gauginos that kinetically mix with hypercharge. There, we will assume that the gauge group remains unbroken, similar to the Standard Model U(1){sub em}. We study different kinds of cosmological bounds, including bounds from thermal overproduction, from primordial nucleosynthesis and from structure formation. Furthermore, we study the possible cosmic-ray signatures predicted by this scenario, with emphasis on the electron and positron channel in light of the recent observations by PAMELA and Fermi LAT. Moreover we study the cosmic-ray signatures of decaying dark matter independently of concrete particle-physics models. In particular we analyze in how far the rise in the positron fraction above 10 GeV, as observed by PAMELA, can be explained by dark matter decay. Lastly, we concentrate on related predictions for gamma-ray observations with the Fermi LAT, and propose to use the dipole-like anisotropy of the prompt gamma-ray dark matter signal to distinguish exotic dark matter contributions from the extragalactic gamma-ray background. (orig.)

  11. Eötvös bounds on couplings of fundamental parameters to gravity.

    Science.gov (United States)

    Dent, Thomas

    2008-07-25

    The possible dependence of fundamental couplings and mass ratios on the gravitational potential has been bounded by comparing atomic clock frequencies over Earth's elliptical orbit. Here we evaluate bounds on such a dependence from Eötvös-type experiments that test the weak equivalence principle, including previously neglected contributions from nuclear binding energy. We find that variations of fundamental parameters correlated with the gravitational potential are limited at 10(-8)-10(-9), an improvement of 2-3 orders of magnitude over atomic clock bounds.

  12. Lower bounds in differential privacy

    OpenAIRE

    De, Anindya

    2011-01-01

    This is a paper about private data analysis, in which a trusted curator holding a confidential database responds to real vector-valued queries. A common approach to ensuring privacy for the database elements is to add appropriately generated random noise to the answers, releasing only these {\\em noisy} responses. In this paper, we investigate various lower bounds on the noise required to maintain different kind of privacy guarantees.

  13. Geometry of Homogeneous Bounded Domains

    CERN Document Server

    Vesentini, E

    2011-01-01

    This title includes: S.G. Gindikin, I.I. Pjateckii-Sapiro, E.B. Vinberg: Homogeneous Kahler manifolds; S.G. Greenfield: Extendibility properties of real submanifolds of Cn; W. Kaup: Holomorphische Abbildungen in Hyperbolische Raume; A. Koranyi: Holomorphic and harmonic functions on bounded symmetric domains; J.L. Koszul: Formes harmoniques vectorielles sur les espaces localement symetriques; S. Murakami: Plongements holomorphes de domaines symetriques; and E.M. Stein: The analogues of Fatous' theorem and estimates for maximal functions.

  14. Wronskian method for bound states

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, Francisco M, E-mail: fernande@quimica.unlp.edu.ar [INIFTA (UNLP, CONICET), Division Quimica Teorica, Boulevard 113 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)

    2011-05-15

    We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider an exactly solvable model, the Gaussian potential well, and a two-well potential proposed earlier for the interpretation of the infrared spectrum of ammonia.

  15. Neutron bound beta-decay: BOB

    Science.gov (United States)

    McAndrew, Josephine; Paul, Stephan; Emmerich, Ralf; Engels, Ralf; Fierlinger, Peter; Gabriel, Mirko; Gutsmiedl, Erwin; Mellenthin, Johannes; Schön, Johannes; Schott, Wolfgang; Ulrich, Andreas; Grüenauer, Florian; Röhrmoser, Anton

    2012-05-01

    An experiment to observe the bound beta-decay (BOB) of the free neutron into a hydrogen atom and an electron anti-neutrino is described. The hyperfine spin state population of the monoenergetic hydrogen atom yields the neutrino left-handedness or possible right-handed admixture as well as possible small scalar and tensor contributions to the weak force. The BOB H(2s) hyperfine states can be separated with a Lamb-Shift Spin Filter. These monoenergetic H(2s) atoms are ionised into H- by charge exchanging within an argon cell. These ions are then separated using an adaptation of a MAC-E Filter. A first experiment is proposed at the FRMII high thermal-neutron flux beam reactor SR6 through-going beam tube, where we will seek to observe this rare neutron decay-mode for the first time and determine the branching ratio. After successful completion, the hyperfine spin state population will be determined, possibly at the ILL high-flux beam reactor through-going beam tube H6-H7, where the thermal neutron flux is a factor of four larger.

  16. Anisotropy-induced photonic bound states in the continuum

    Science.gov (United States)

    Gomis-Bresco, Jordi; Artigas, David; Torner, Lluis

    2017-03-01

    Bound states in the continuum (BICs) are radiationless localized states embedded in the part of the parameter space that otherwise corresponds to radiative modes. Many decades after their original prediction and early observations in acoustic systems, such states have been demonstrated recently in photonic structures with engineered geometries. Here, we put forward a mechanism, based on waveguiding structures that contain anisotropic birefringent materials, that affords the existence of BICs with fundamentally new properties. In particular, anisotropy-induced BICs may exist in symmetric as well as in asymmetric geometries; they may form in tunable angular propagation directions; their polarization may be pure transverse electric, pure transverse magnetic or full vector with tunable polarization hybridity; and they may be the only possible bound states of properly designed structures, and thus appear as a discrete, isolated bound state embedded in a whole sea of radiative states.

  17. Cyclotron transitions of bound ions

    Science.gov (United States)

    Bezchastnov, Victor G.; Pavlov, George G.

    2017-06-01

    A charged particle in a magnetic field possesses discrete energy levels associated with particle rotation around the field lines. The radiative transitions between these levels are the well-known cyclotron transitions. We show that a bound complex of particles with a nonzero net charge displays analogous transitions between the states of confined motion of the entire complex in the field. The latter bound-ion cyclotron transitions are affected by a coupling between the collective and internal motions of the complex and, as a result, differ from the transitions of a "reference" bare ion with the same mass and charge. We analyze the cyclotron transitions for complex ions by including the coupling within a rigorous quantum approach. Particular attention is paid to comparison of the transition energies and oscillator strengths to those of the bare ion. Selection rules based on integrals of collective motion are derived for the bound-ion cyclotron transitions analytically, and the perturbation and coupled-channel approaches are developed to study the transitions quantitatively. Representative examples are considered and discussed for positive and negative atomic and cluster ions.

  18. Bounds on collapse models from cold-atom experiments

    Science.gov (United States)

    Bilardello, Marco; Donadi, Sandro; Vinante, Andrea; Bassi, Angelo

    2016-11-01

    The spontaneous localization mechanism of collapse models induces a Brownian motion in all physical systems. This effect is very weak, but experimental progress in creating ultracold atomic systems can be used to detect it. In this paper, we considered a recent experiment (Kovachy et al., 2015), where an atomic ensemble was cooled down to picokelvins. Any Brownian motion induces an extra increase of the position variance of the gas. We study this effect by solving the dynamical equations for the Continuous Spontaneous Localizations (CSL) model, as well as for its non-Markovian and dissipative extensions. The resulting bounds, with a 95 % of confidence level, are beaten only by measurements of spontaneous X-ray emission and by experiments with cantilever (in the latter case, only for rC ≥ 10-7 m, where rC is one of the two collapse parameters of the CSL model). We show that, contrary to the bounds given by X-ray measurements, non-Markovian effects do not change the bounds, for any reasonable choice of a frequency cutoff in the spectrum of the collapse noise. Therefore the bounds here considered are more robust. We also show that dissipative effects are unimportant for a large spectrum of temperatures of the noise, while for low temperatures the excluded region in the parameter space is the more reduced, the lower the temperature.

  19. Optimal Weak Lensing Skewness Measurements

    OpenAIRE

    Zhang, Tong-Jie; Pen, Ue-Li; Zhang, Pengjie; Dubinski, John

    2003-01-01

    Weak lensing measurements are entering a precision era to statistically map the distribution of matter in the universe. The most common measurement has been of the variance of the projected surface density of matter, which corresponds to the induced correlation in alignments of background galaxies. This measurement of the fluctuations is insensitive to the total mass content, like using waves on the ocean to measure its depths. But when the depth is shallow as happens near a beach, waves beco...

  20. Weak neutral-current interactions

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, R.M.

    1978-08-01

    The roles of each type of experiment in establishing uniquely the values of the the neutral-current couplings of u and d quarks are analyzed together with their implications for gauge models of the weak and electromagnetic interactions. An analysis of the neutral-current couplings of electrons and of the data based on the assumption that only one Z/sup 0/ boson exists is given. Also a model-independent analysis of parity violation experiments is discussed. 85 references. (JFP)

  1. Rare weak decays of η'→K π

    Science.gov (United States)

    Gao, Dao-Neng

    2017-11-01

    Rare weak decays of η'→K π have been investigated in the framework of the U (3 ) chiral perturbation theory at the leading order. Our study shows that the branching ratio B (η'→K π ) is of the order of 10-11, which is far below the present experimental upper bound given by the BESIII Collaboration. By further analysis of η'→K+π- and η'→K0π0, the ratio of isospin amplitudes is found, |A1 /2/A3 /2|≃35 , which supports that the Δ I =1 /2 transition enhancement, namely, the Δ I =1 /2 rule, could be functional in η' weak decays.

  2. Some Properties of Solutions to Weakly Hypoelliptic Equations

    Directory of Open Access Journals (Sweden)

    Christian Bär

    2013-01-01

    Full Text Available A linear different operator L is called weakly hypoelliptic if any local solution u of Lu=0 is smooth. We allow for systems, that is, the coefficients may be matrices, not necessarily of square size. This is a huge class of important operators which coverall elliptic, overdetermined elliptic, subelliptic, and parabolic equations. We extend several classical theorems from complex analysis to solutions of any weakly hypoelliptic equation: the Montel theorem providing convergent subsequences, the Vitali theorem ensuring convergence of a given sequence, and Riemann's first removable singularity theorem. In the case of constant coefficients, we show that Liouville's theorem holds, any bounded solution must be constant, and any Lp-solution must vanish.

  3. A weakly constrained $W'$ at the early LHC

    CERN Document Server

    Grojean, Christophe; Torre, Riccardo

    2011-01-01

    We study, within an effective approach, the phenomenology of a charged W' vector which transforms as an isosinglet under the Standard Model gauge group. We discuss bounds from present data, finding that these are quite weak for suitable choices of the right-handed quark mixing matrix. Then we study the resonant production at the early LHC of such a weakly constrained W'. We start discussing the reach in the dijet final state, which is one of the channels where the first W' signal would most likely appear, and then we analyse prospects for the more challenging discovery of W' decays into W{\\gamma} and WZ. We show in particular that the former can be used to gain insight on the possibly composite nature of the resonance.

  4. [Muscle weakness in cerebral palsy].

    Science.gov (United States)

    Givon, Uri

    2009-01-01

    Over the last two decades, muscle weakness has been shown to be a major component of cerebral palsy (CP) pathology. Caused by multiple etiologies including variations in the muscle fiber type, pathologic motor unit function, co-contraction of agonists and antagonists, and muscle size and rigidity, weakness interferes with function and leads to limited function and participation. Muscle strength was found to be associated with walking ability and with functional scales. Children with CP were found to be weaker than typically developing children, and differences were found with respect to muscle groups in children with CP. Muscle weakness should be evaluated as objectively as possible to improve the quality of diagnosis and treatment. Manual muscle testing is not sufficient for evaluation, and instrumented muscle testing is validated in CP. Muscle strengthening is an important part of treatment of CP. Several methods of strengthening have been described. Muscle lengthening and other spasticity-modifying therapies have been shown to have a positive effect on muscle strength. Children who participated in muscle strengthening programs had a better quality of life and improved function.

  5. Completely continuous and weakly completely continuous abstract ...

    Indian Academy of Sciences (India)

    if the operator ρa of right multiplication by a is compact (weakly compact, respectively). An algebra A is called right completely continuous (right weakly completely continuous) if any element a ∈ A is right completely continuous (right weakly completely con- tinuous, respectively). Left completely continuous (left weakly ...

  6. Strength and Weakness of Animal Vaccine Industry in China

    OpenAIRE

    Xie, Hong-hai; Wang, Geng-xin

    2010-01-01

    Based on the introduction of the status of animal vaccine industry in China, the strength, weakness, opportunity and threat of animal vaccine industry is analyzed by SWOT. Among them, strength is mainly reflected in the broad market, and the favorable industrial policy and development environment. Weakness is the irrational structure of product, the nonstandard production inspection, and the irregular market. Opportunity is mainly reflected in improving government’s emphasis on animal secur...

  7. Tunneling Time and Weak Measurement in Strong Field Ionization

    Science.gov (United States)

    Zimmermann, Tomáš; Mishra, Siddhartha; Doran, Brent R.; Gordon, Daniel F.; Landsman, Alexandra S.

    2016-06-01

    Tunneling delays represent a hotly debated topic, with many conflicting definitions and little consensus on when and if such definitions accurately describe the physical observables. Here, we relate these different definitions to distinct experimental observables in strong field ionization, finding that two definitions, Larmor time and Bohmian time, are compatible with the attoclock observable and the resonance lifetime of a bound state, respectively. Both of these definitions are closely connected to the theory of weak measurement, with Larmor time being the weak measurement value of tunneling time and Bohmian trajectory corresponding to the average particle trajectory, which has been recently reconstructed using weak measurement in a two-slit experiment [S. Kocsis, B. Braverman, S. Ravets, M. J. Stevens, R. P. Mirin, L. K. Shalm, and A. M. Steinberg, Science 332, 1170 (2011)]. We demonstrate a big discrepancy in strong field ionization between the Bohmian and weak measurement values of tunneling time, and we suggest this arises because the tunneling time is calculated for a small probability postselected ensemble of electrons. Our results have important implications for the interpretation of experiments in attosecond science, suggesting that tunneling is unlikely to be an instantaneous process.

  8. Weak convergence of Jacobian determinants under asymmetric assumptions

    Directory of Open Access Journals (Sweden)

    Teresa Alberico

    2012-05-01

    Full Text Available Let $\\Om$ be a bounded open set in $\\R^2$ sufficiently smooth and $f_k=(u_k,v_k$ and $f=(u,v$ mappings belong to the Sobolev space $W^{1,2}(\\Om,\\R^2$. We prove that if the sequence of Jacobians $J_{f_k}$ converges to a measure $\\mu$ in sense of measures andif one allows different assumptions on the two components of $f_k$ and $f$, e.g.$$u_k \\rightharpoonup u \\;\\;\\mbox{weakly in} \\;\\; W^{1,2}(\\Om \\qquad \\, v_k \\rightharpoonup v \\;\\;\\mbox{weakly in} \\;\\; W^{1,q}(\\Om$$for some $q\\in(1,2$, then\\begin{equation}\\label{0}d\\mu=J_f\\,dz.\\end{equation}Moreover, we show that this result is optimal in the sense that conclusion fails for $q=1$.On the other hand, we prove that \\eqref{0} remains valid also if one considers the case $q=1$, but it is necessary to require that $u_k$ weakly converges to $u$ in a Zygmund-Sobolev space with a slightly higher degree of regularity than $W^{1,2}(\\Om$ and precisely$$ u_k \\rightharpoonup u \\;\\;\\mbox{weakly in} \\;\\; W^{1,L^2 \\log^\\alpha L}(\\Om$$for some $\\alpha >1$.    

  9. On the Weak Computability of Continuous Real Functions

    Directory of Open Access Journals (Sweden)

    Matthew S. Bauer

    2010-06-01

    Full Text Available In computable analysis, sequences of rational numbers which effectively converge to a real number x are used as the (rho- names of x. A real number x is computable if it has a computable name, and a real function f is computable if there is a Turing machine M which computes f in the sense that, M accepts any rho-name of x as input and outputs a rho-name of f(x for any x in the domain of f. By weakening the effectiveness requirement of the convergence and classifying the converging speeds of rational sequences, several interesting classes of real numbers of weak computability have been introduced in literature, e.g., in addition to the class of computable real numbers (EC, we have the classes of semi-computable (SC, weakly computable (WC, divergence bounded computable (DBC and computably approximable real numbers (CA. In this paper, we are interested in the weak computability of continuous real functions and try to introduce an analogous classification of weakly computable real functions. We present definitions of these functions by Turing machines as well as by sequences of rational polygons and prove these two definitions are not equivalent. Furthermore, we explore the properties of these functions, and among others, show their closure properties under arithmetic operations and composition.

  10. Lower bounds for randomized Exclusive Write PRAMs

    Energy Technology Data Exchange (ETDEWEB)

    MacKenzie, P.D.

    1995-05-02

    In this paper we study the question: How useful is randomization in speeding up Exclusive Write PRAM computations? Our results give further evidence that randomization is of limited use in these types of computations. First we examine a compaction problem on both the CREW and EREW PRAM models, and we present randomized lower bounds which match the best deterministic lower bounds known. (For the CREW PRAM model, the lower bound is asymptotically optimal.) These are the first non-trivial randomized lower bounds known for the compaction problem on these models. We show that our lower bounds also apply to the problem of approximate compaction. Next we examine the problem of computing boolean functions on the CREW PRAM model, and we present a randomized lower bound, which improves on the previous best randomized lower bound for many boolean functions, including the OR function. (The previous lower bounds for these functions were asymptotically optimal, but we improve the constant multiplicative factor.) We also give an alternate proof for the randomized lower bound on PARITY, which was already optimal to within a constant additive factor. Lastly, we give a randomized lower bound for integer merging on an EREW PRAM which matches the best deterministic lower bound known. In all our proofs, we use the Random Adversary method, which has previously only been used for proving lower bounds on models with Concurrent Write capabilities. Thus this paper also serves to illustrate the power and generality of this method for proving parallel randomized lower bounds.

  11. Information-theoretic measures of hydrogen-like ions in weakly coupled Debye plasmas

    Science.gov (United States)

    Zan, Li Rong; Jiao, Li Guang; Ma, Jia; Ho, Yew Kam

    2017-12-01

    Recent development of information theory provides researchers an alternative and useful tool to quantitatively investigate the variation of the electronic structure when atoms interact with the external environment. In this work, we make systematic studies on the information-theoretic measures for hydrogen-like ions immersed in weakly coupled plasmas modeled by Debye-Hückel potential. Shannon entropy, Fisher information, and Fisher-Shannon complexity in both position and momentum spaces are quantified in high accuracy for the hydrogen atom in a large number of stationary states. The plasma screening effect on embedded atoms can significantly affect the electronic density distributions, in both conjugate spaces, and it is quantified by the variation of information quantities. It is shown that the composite quantities (the Shannon entropy sum and the Fisher information product in combined spaces and Fisher-Shannon complexity in individual space) give a more comprehensive description of the atomic structure information than single ones. The nodes of wave functions play a significant role in the changes of composite information quantities caused by plasmas. With the continuously increasing screening strength, all composite quantities in circular states increase monotonously, while in higher-lying excited states where nodal structures exist, they first decrease to a minimum and then increase rapidly before the bound state approaches the continuum limit. The minimum represents the most reduction of uncertainty properties of the atom in plasmas. The lower bounds for the uncertainty product of the system based on composite information quantities are discussed. Our research presents a comprehensive survey in the investigation of information-theoretic measures for simple atoms embedded in Debye model plasmas.

  12. Identification and classification of weak layers in the snow

    Directory of Open Access Journals (Sweden)

    E. S. Klimenko

    2013-01-01

    Full Text Available The paper considers the role of vertical snowpack structure for snow avalanche formation and describes the idea of «structural instability». It aims at enhancing the knowledge about transition mechanisms between stable and unstable states of snowpack and snow avalanches release. Structural instability implies the presence of weak layer or interface in vertical snowpack profile. Type of snow failure and avalanche characteristics are completely defined by snowpack state and properties. Thus wide variety of genetic types of snow avalanches indicates the existence of structural instability of different types. The detailed analysis of scientific publications and field observations led to the creation of a new classification of weak layers. The layers are classified basing on their cohesiveness, the causes of initial disturbance and internal and external processes which form a weak layer. The classification is a necessary part of global method which allows assessing snowpack stability using modern physical models of snow cover evolution.

  13. Protecting weak measurements against systematic errors

    OpenAIRE

    Pang, Shengshi; Alonso, Jose Raul Gonzalez; Brun, Todd A.; Jordan, Andrew N.

    2016-01-01

    In this work, we consider the systematic error of quantum metrology by weak measurements under decoherence. We derive the systematic error of maximum likelihood estimation in general to the first-order approximation of a small deviation in the probability distribution, and study the robustness of standard weak measurement and postselected weak measurements against systematic errors. We show that, with a large weak value, the systematic error of a postselected weak measurement when the probe u...

  14. On the dynamic buckling of a weakly damped nonlinear elastic ...

    African Journals Online (AJOL)

    In this paper we determine the dynamic buckling load of a strictly nonlinear but weakly damped elastic oscillatory model structure subjected to small perturbations The loading history is explicitly time dependent and varies slowly with time over a natural period of oscillation of the structure. A multiple timing regular ...

  15. The role of weak intermolecular CH… F interactions in ...

    Indian Academy of Sciences (India)

    Analysis of Cambridge Structural Database using these newly defined parameters reveals high propensity of C-H…F interactions in organic crystals. The present structural study suggests much larger role of fluorine driven intermolecular interactions that are even though weak, but possess significant ability to direct and alter ...

  16. Towards Automatic Resource Bound Analysis for OCaml

    OpenAIRE

    Hoffmann, Jan; Das, Ankush; Weng, Shu-Chun

    2016-01-01

    This article presents a resource analysis system for OCaml programs. This system automatically derives worst-case resource bounds for higher-order polymorphic programs with user-defined inductive types. The technique is parametric in the resource and can derive bounds for time, memory allocations and energy usage. The derived bounds are multivariate resource polynomials which are functions of different size parameters that depend on the standard OCaml types. Bound inference is fully automatic...

  17. Distance hijacking attacks on distance bounding protocols

    OpenAIRE

    Cremers, Cas; Rasmussen, Kasper Bonne; Čapkun, Srdjan

    2011-01-01

    Distance bounding protocols are typically analyzed with respect to three types of attacks: Distance Fraud, Mafia Fraud, and Terrorist Fraud. We define and analyze a fourth main type of attack on distance bounding protocols, called Distance Hijacking. We show that many proposed distance bounding protocols are vulnerable to this type of attack, and we propose solutions to make these protocols resilient to Distance Hijacking. We further show that verifying distance bounding protocols using exist...

  18. Purity- and Gaussianity-bounded uncertainty relations

    Science.gov (United States)

    Mandilara, A.; Karpov, E.; Cerf, N. J.

    2014-01-01

    Bounded uncertainty relations provide the minimum value of the uncertainty assuming some additional information on the state. We derive analytically an uncertainty relation bounded by a pair of constraints, those of purity and Gaussianity. In a limiting case this uncertainty relation reproduces the purity-bounded derived by Man’ko and Dodonov and the Gaussianity-bounded one (Mandilara and Cerf 2012 Phys. Rev. A 86 030102R).

  19. Weak polyelectrolytes in Confined Geometries

    Science.gov (United States)

    Whitmer, Jonathan K.; Rathee, Vikramjit S.; Sikora, Benjamin

    Crucial to the behavior of recently designed charge-rejection and mosaic membranes are the conformations of polyelectrolyte brushes and oligomeric grafts used to control the membranes' surface charge. The use of pH-tunable weak polyelectrolytes with associative interactions enables fine tuning of material transport properties. Here, we apply constant-pH molecular dynamics along with free energy sampling algorithms to understand the subtle tug-of-war between pH, salt concentrations, and solvation forces in confined systems, and determine how each of these effects alters transport within the system. We further discuss the implications of our findings for the design of electrolyte separation membranes.

  20. The effect of parents' schooling on child's schooling: a nonparametric bounds analysis

    NARCIS (Netherlands)

    de Haan, M.

    2011-01-01

    A positive relation between parents’ schooling and child’s schooling does not necessarily reflect a causal relation. This article uses a new approach to identify intergenerational schooling effects: a nonparametric bounds analysis. By relying on relatively weak and in part testable assumptions, this

  1. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    Massaro, D.

    2012-01-01

    This thesis studies the effect of individual bounded rationality on aggregate macroeconomic dynamics. Boundedly rational agents are specified as using simple heuristics in their decision making. An important aspect of the type of bounded rationality described in this thesis is that the population of

  2. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil

    2014-01-01

    graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...

  3. Upper bound on quantum stabilizer codes

    Science.gov (United States)

    Li, Zhuo; Xing, Li-Juan

    2009-03-01

    By studying sets of operators having constant weight, we present an analytical upper bound on the pure quantum stabilizer codes whose underlying quantum system can be of arbitrary dimension, which outperforms the well-known quantum Hamming bound, the optimal analytical upper bound so far for small code length.

  4. Cobalt(III) complexes of monodentate N9-bound adeninate (ade-), [Co(ade-kappaN9)Cl(en)2]+ (en = 1,2-diaminoethane): syntheses, crystal structures, and protonation behaviors of the geometrical isomers.

    Science.gov (United States)

    Suzuki, Takayoshi; Hirai, Yoko; Monjushiro, Hideaki; Kaizaki, Sumio

    2004-10-04

    In acidic aqueous solution, a cobalt(III) complex containing monodentate N(9)-bound adeninate (ade(-)), cis-[Co(ade-kappaN(9))Cl(en)(2)]Cl (cis-[1]Cl), underwent protonation to the adeninate moiety without geometrical isomerization or decomposition of the Co(III) coordination sphere, and complexes of cis-[CoCl(Hade)(en)(2)]Cl(2) (cis-[2]Cl(2)) and cis-[Co(H(2)ade)Cl(en)(2)]Cl(3) (cis-[3]Cl(3)) could be isolated. The pK(a) values of the Hade and H(2)ade(+) complexes are 6.03(1) and 2.53(12), respectively, at 20 degrees C in 0.1 M aqueous NaCl. The single-crystal X-ray analyses of cis-[2]Cl(2).0.5H(2)O and cis-[3]Cl(2)(BF(4)).H(2)O revealed that protonation took place first at the adeninate N(7) and then at the N(1) atoms to form adenine tautomer (7H-Hade-kappaN(9)) and cationic adeninium (1H,7H-H(2)ade(+)-kappaN(9)) complexes, respectively. On the other hand, addition of NaOH to an aqueous solution of cis-[1]Cl afforded a mixture of geometrical isomers of the hydroxo-adeninato complex, cis- and trans-[Co(ade-kappaN(9))(OH)(en)(2)](+). The trans-isomer of chloro-adeninato complex trans-[Co(ade-kappaN(9))Cl(en)(2)]BF(4) (trans-[1]BF(4)) was synthesized by a reaction of cis-[2](BF(4))(2) and sodium methoxide in methanol. This isomer in acidic aqueous solution was also stable toward isomerization, affording the corresponding adenine tautomer and adeninium complexes (pK(a) = 5.21(1) and 2.48(9), respectively, at 20 degrees C in 0.1 M aqueous NaCl). The protonated product of trans-[Co(7H-Hade-kappaN(9))Cl(en)(2)](BF(4))(2).H(2)O (trans-[2](BF(4))(2).H(2)O) could also be characterized by X-ray analysis. Furthermore, the hydrogen-bonding interactions of the adeninate/adenine tautomer complexes cis-[1]BF(4), cis-[2](BF(4))(2), and trans-[2](BF(4))(2) with 1-cyclohexyluracil in acetonitrile-d(3) were investigated by (1)H NMR spectroscopy. The crystal structure of trans-[Co(ade)(H(2)O)(en)(2)]HPO(4).3H(2)O, which was obtained by a reaction of trans-[Co(ade)(OH)(en)(2)]BF(4

  5. Planckian axions and the Weak Gravity Conjecture

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, Thomas C.; Long, Cody; McAllister, Liam [Department of Physics, Cornell University,Ithaca, NY 14853 (United States)

    2016-01-18

    Several recent works http://dx.doi.org/10.1088/1475-7516/2015/09/020, http://dx.doi.org/10.1007/JHEP08(2015)032, http://dx.doi.org/10.1007/JHEP10(2015)023 have claimed that the Weak Gravity Conjecture (WGC) excludes super-Planckian displacements of axion fields, and hence large-field axion inflation, in the absence of monodromy. We argue that in theories with N≫1 axions, super-Planckian axion diameters D are readily allowed by the WGC. We clarify the nontrivial relationship between the kinetic matrix K — unambiguously defined by its form in a Minkowski-reduced basis — and the diameter of the axion fundamental domain, emphasizing that in general the diameter is not solely determined by the eigenvalues f{sub 1}{sup 2}≤…≤f{sub N}{sup 2} of K: the orientations of the eigenvectors with respect to the identifications imposed by instantons must be incorporated. In particular, even if one were to impose the condition f{sub N}bounded from below by S≥SM{sub pl}/f{sub N}, with S a fixed constant, but in the universal limit S≳S√NM{sub pl}/f{sub N}. Thus, having f{sub N}>M{sub pl} does not immediately imply the existence of unsuppressed higher harmonic contributions to the potential. Finally, we argue that in effective axion-gravity theories, the zero-form version of the WGC can be satisfied by gravitational instantons that make negligible contributions to the potential.

  6. Weak lensing and cosmological investigation

    CERN Document Server

    Acquaviva, V

    2005-01-01

    In the last few years the scientific community has been dealing with the challenging issue of identifying the dark energy component. We regard weak gravitational lensing as a brand new, and extremely important, tool for cosmological investigation in this field. In fact, the features imprinted on the cosmic microwave background radiation by the lensing from the intervening distribution of matter represent a pretty unbiased estimator, and can thus be used for putting constraints on different dark energy models. This is true in particular for the magnetic-type B-modes of CMB polarization, whose unlensed spectrum at large multipoles (l approximately=1000) is very small even in presence of an amount of gravitational waves as large as currently allowed by the experiments: therefore, on these scales the lensing phenomenon is the only responsible for the observed power, and this signal turns out to be a faithful tracer of the dark energy dynamics. We first recall the formal apparatus of the weak lensing in extended t...

  7. Time—periodic weak solutions

    Directory of Open Access Journals (Sweden)

    Eliana Henriques de Brito

    1990-01-01

    Full Text Available In continuing from previous papers, where we studied the existence and uniqueness of the global solution and its asymptotic behavior as time t goes to infinity, we now search for a time-periodic weak solution u(t for the equation whose weak formulation in a Hilbert space H isddt(u′,v+δ(u′,v+αb(u,v+βa(u,v+(G(u,v=(h,vwhere: ′=d/dt; (′ is the inner product in H; b(u,v, a(u,v are given forms on subspaces U⊂W, respectively, of H; δ>0, α≥0, β≥0 are constants and α+β>0; G is the Gateaux derivative of a convex functional J:V⊂H→[0,∞ for V=U, when α>0 and V=W when α=0, hence β>0; v is a test function in V; h is a given function of t with values in H.

  8. Political corruption and weak state

    Directory of Open Access Journals (Sweden)

    Stojiljković Zoran

    2013-01-01

    Full Text Available The author starts from the hypothesis that it is essential for the countries of the region to critically assess the synergy established between systemic, political corruption and a selectively weak, “devious” nature of the state. Moreover, the key dilemma is whether the expanded practice of political rent seeking supports the conclusion that the root of all corruption is in the very existence of the state - particularly in excessive, selective and deforming state interventions and benefits that create a fertile ground for corruption? The author argues that the destructive combination of weak government and rampant political corruption is based on scattered state intervention, while also rule the parties cartel in the executive branch subordinate to parliament, the judiciary and the police. Corrupt exchange takes place with the absence of strong institutional framework and the precise rules of the political and electoral games, control of public finances and effective political and anti-monopoly legislation and practice included. Exit from the current situation can be seen in the realization of effective anti­corruption strategy that integrates preventive and repressive measures and activities and lead to the establishment of principles of good governance. [Projekat Ministarstva nauke Republike Srbije, br. 179076: Politički identitet Srbije u regionalnom i globalnom kontekstu

  9. First results of the CERN Resonant Weakly Interacting sub-eV Particle Search (CROWS)

    CERN Document Server

    Betz, M; Gasior, M; Thumm, M; Rieger, S W

    2013-01-01

    The CERN Resonant Weakly Interacting sub-eV Particle Search probes the existence of weakly interacting sub-eV particles like axions or hidden sector photons. It is based on the principle of an optical light shining through the wall experiment, adapted to microwaves. Critical aspects of the experiment are electromagnetic shielding, design and operation of low loss cavity resonators, and the detection of weak sinusoidal microwave signals. Lower bounds are set on the coupling constant g=4.5 x 10$^{-8}$ GeV$^{-1}$ for axionlike particles with a mass of m$_a$=7.2 $\\mu$eV. For hidden sector photons, lower bounds are set for the coupling constant $\\chi$=4.1 x 10$^{^-9}$ at a mass of m$\\gamma$=10.8 $\\mu$eV. For the latter we are probing a previously unexplored region in the parameter space.

  10. A Search for Gravitationally Bound Cloud Cores within the CMZ

    Science.gov (United States)

    Gehret, Elizabeth; Battersby, Cara

    2016-01-01

    In general, current star formation theories successfully model the rate at which stars are forming throughout our Galaxy as well as others, with the star formation rate (SFR) in a given region being proportional to the amount of gas above a threshold density. The Central Molecular Zone (CMZ) of our Galaxy is an excellent place to test these models. It is home to the highest amount of dense, molecular gas within our Galaxy-and yet, the SFR within this region is an order of magnitude lower than would be expected using current star formation models. This project utilizes data taken from the SMA Legacy Survey of the CMZ, in a search for gravitationally bound structures within three small gas clouds near the Galactic Center, as well as the 1.6 degree cloud. Dense gas structures are detected using H2CO-a dense gas tracer, and 1.3mm cold, dust continuum. These regions are catalogued using dendrograms to identify which structures have continuous and significant H2CO emission. Gravitationally bound candidates were identified by deriving each structure's virial ratio. Within the three clouds near the GC, 40 structures were catalogued, with one structure that was found to be gravitationally bound. Very large virial ratios are the result of large H2CO line widths, possibly due to a high degree of tidal compression. This analysis is also performed on the 1.6 degree cloud, in a region with two suspected bound cores. One of these two cores is close to virial equilibrium and likely gravitationally bound, thus providing support for the use of this method on other clouds within the CMZ. This work supported in part by the NSF REU and DoD ASSURE programs under grant no. 1262851 and by the Smithsonian Institution.

  11. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas

    2016-01-01

    A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.

  12. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan

    2014-10-07

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  13. Synchronizability of nonidentical weakly dissipative systems

    Science.gov (United States)

    Sendiña-Nadal, Irene; Letellier, Christophe

    2017-10-01

    Synchronization is a very generic process commonly observed in a large variety of dynamical systems which, however, has been rarely addressed in systems with low dissipation. Using the Rössler, the Lorenz 84, and the Sprott A systems as paradigmatic examples of strongly, weakly, and non-dissipative chaotic systems, respectively, we show that a parameter or frequency mismatch between two coupled such systems does not affect the synchronizability and the underlying structure of the joint attractor in the same way. By computing the Shannon entropy associated with the corresponding recurrence plots, we were able to characterize how two coupled nonidentical chaotic oscillators organize their dynamics in different dissipation regimes. While for strongly dissipative systems, the resulting dynamics exhibits a Shannon entropy value compatible with the one having an average parameter mismatch, for weak dissipation synchronization dynamics corresponds to a more complex behavior with higher values of the Shannon entropy. In comparison, conservative dynamics leads to a less rich picture, providing either similar chaotic dynamics or oversimplified periodic ones.

  14. Half-collision analysis of far-wing diffuse structure in Cs-Xe

    Science.gov (United States)

    Exton, R. J.; Hillard, M. E.; Lempert, W. R.

    1987-01-01

    Laser excitation in the far red wing of the second principal series doublet of Cs mixed with Xe revealed a diffuse structure associated with the 2P(3/2) component. The structure is thought to originate from a reflection type of spectrum between the weakly bound E 2Sigma(1/2) excited state and the X 2Sigma(1/2) repulsive ground state of CsXe.

  15. Performance Bounds of Quaternion Estimators.

    Science.gov (United States)

    Xia, Yili; Jahanchahi, Cyrus; Nitta, Tohru; Mandic, Danilo P

    2015-12-01

    The quaternion widely linear (WL) estimator has been recently introduced for optimal second-order modeling of the generality of quaternion data, both second-order circular (proper) and second-order noncircular (improper). Experimental evidence exists of its performance advantage over the conventional strictly linear (SL) as well as the semi-WL (SWL) estimators for improper data. However, rigorous theoretical and practical performance bounds are still missing in the literature, yet this is crucial for the development of quaternion valued learning systems for 3-D and 4-D data. To this end, based on the orthogonality principle, we introduce a rigorous closed-form solution to quantify the degree of performance benefits, in terms of the mean square error, obtained when using the WL models. The cases when the optimal WL estimation can simplify into the SWL or the SL estimation are also discussed.

  16. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan

    2001-01-01

    Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...

  17. Weak transitions in lattice QCD

    Energy Technology Data Exchange (ETDEWEB)

    Maturana, G.

    1984-01-01

    Some techniques to calculate the effects of the strong interactions on the matrix elements of weak processes are described. The lattice formulation of Quantum Chromodynamics is used to account for the low energy gluons, and the corresponding numerical methods are explained. The high energy contributions are included in effective lagrangians and the problem of matching the different scales related to the renormalization of the operators and wavefunctions is also discussed. The ..delta..l = 1/2 enhancement rule and the K/sup 0/-anti-K/sup 0/ are used to illustrate these techniques and the results of a numerical calculation is reported. The values obtained are very encouraging and they certainly show good qualitative agreement with the experimental values. The emphasis is on general techniques, and in particular, several improvements to this particular calculation are proposed.

  18. Strengths, weaknesses, opportunities and threats

    DEFF Research Database (Denmark)

    Bull, Joseph William; Jobstvogt, N.; Böhnke-Henrichs, A.

    2016-01-01

    The ecosystem services concept (ES) is becoming a cornerstone of contemporary sustainability thought. Challenges with this concept and its applications are well documented, but have not yet been systematically assessed alongside strengths and external factors that influence uptake. Such an assess......The ecosystem services concept (ES) is becoming a cornerstone of contemporary sustainability thought. Challenges with this concept and its applications are well documented, but have not yet been systematically assessed alongside strengths and external factors that influence uptake....... Such an assessment could form the basis for improving ES thinking, further embedding it into environmental decisions and management.The Young Ecosystem Services Specialists (YESS) completed a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of ES through YESS member surveys. Strengths include the approach...

  19. On order bounded subsets of locally solid Riesz spaces | Hong ...

    African Journals Online (AJOL)

    In a topological Riesz space there are two types of bounded subsets: order bounded subsets and topologically bounded subsets. It is natural to ask (1) whether an order bounded subset is topologically bounded and (2) whether a topologically bounded subset is order bounded. A classical result gives a partial answer to (1) ...

  20. Fault zone fabric and fault weakness

    NARCIS (Netherlands)

    Collettini, C.; Niemeijer, A.; Viti, C.; Marone, C.

    2009-01-01

    Geological and geophysical evidence suggests that some crustal faults are weak1–6 compared to laboratory measurements of frictional strength7. Explanations for fault weakness include the presence of weak minerals4, high fluid pressures within the fault core8,9 and dynamic processes such as