Science.gov

Sample records for residual two-body interaction

  1. Pseudopotential treatment of two body interactions

    NASA Astrophysics Data System (ADS)

    Kanjilal, Krittika

    Ultracold atomic gases have been of great theoretical and experimental interest in the last two decades. In these systems, the de Broglie wavelength of the particles is much greater than the two body van der Waals length. As a result, the details of the two body interaction potential are irrelevant for a large number of applications and the realistic two body interaction potential can be replaced by a simple finite range or zero range model potential that reproduces the scattering quantities of the full interaction potential. This thesis develops zero range pseudopotentials and applies them to trapped two-particle systems. Ultracold gases loaded into optical lattices can be used to realize two particle systems under approximately harmonic confinement. We use pseudopotentials to obtain the eigenspectrum of two particles under external harmonic confinement semi-analytically. Advancements in trapping technology have resulted in the realization of low-dimensional systems. We develop pseudopotentials to treat two body interactions in one and two dimensions. We also elaborate on the physics that is unique to one and two dimensional systems. Feshbach resonances allow for the tunability of the effective two body interaction strength in the presence of a magnetic field. To model Feshbach resonances in two and three dimensions we develop coupled two channel zero range potentials. Dipole-dipole interactions in Chromium and polar molecules have been the subject of a lot of recent research. Unlike the interactions between two alkali atoms, these interactions are long range and anisotropic. We explore the scattering properties of two aligned dipoles using a simple shape dependent model potential. To understand a system two aligned dipoles under confinement, we develop a pseudopotential treatment for cylindrically symmetric interaction potentials under cylindrically symmetric harmonic confinement. This pseudopotential can be used to model any cylindrically symmetric interaction

  2. Separable approximations of two-body interactions

    NASA Astrophysics Data System (ADS)

    Haidenbauer, J.; Plessas, W.

    1983-01-01

    We perform a critical discussion of the efficiency of the Ernst-Shakin-Thaler method for a separable approximation of arbitrary two-body interactions by a careful examination of separable 3S1-3D1 N-N potentials that were constructed via this method by Pieper. Not only the on-shell properties of these potentials are considered, but also a comparison is made of their off-shell characteristics relative to the Reid soft-core potential. We point out a peculiarity in Pieper's application of the Ernst-Shakin-Thaler method, which leads to a resonant-like behavior of his potential 3SD1D. It is indicated where care has to be taken in order to circumvent drawbacks inherent in the Ernst-Shakin-Thaler separable approximation scheme. NUCLEAR REACTIONS Critical discussion of the Ernst-Shakin-Thaler separable approximation method. Pieper's separable N-N potentials examined on shell and off shell.

  3. Multinucleon Ejection Model for Two Body Current Neutrino Interactions

    SciTech Connect

    Sobczyk, Jan T.; /Fermilab

    2012-06-01

    A model is proposed to describe nucleons ejected from a nucleus as a result of two-body-current neutrino interactions. The model can be easily implemented in Monte Carlo neutrino event generators. Various possibilities to measure the two-body-current contribution are discussed. The model can help identify genuine charge current quasielastic events and allow for a better determination of the systematic error on neutrino energy reconstruction in neutrino oscillation experiments.

  4. Unsteady Aerodynamic Interaction between Two Bodies at Hypersonic Speed

    NASA Astrophysics Data System (ADS)

    Ozawa, Hiroshi; Kitamura, Keiichi; Hanai, Katsuhisa; Mori, Koichi; Nakamura, Yoshiaki

    This paper presents experimental results of unsteady aerodynamic interactions including Shock/Shock Interaction (SSI) and Shock/Boundary Layer Interaction (SBLI) between two bodies at hypersonic speed. These interactions can be seen in space vehicles consisting of multi-bodies, such as a TSTO, or at a scramjet engine inlet. The present study considers the effect of a flat plate below the SSI where a boundary-layer is developed on the plate surface. More specifically, the interacted flow for a combination of a flat plate (FP) and a hemi-circular cylinder (HCC) is examined at a hypersonic speed (M∞=8.1) the distributions of surface pressure and heat transfer rate are measured. To obtain various SSI patterns, the clearance between two bodies (FP and HCC) is changed. Results show that unsteadiness at the SSI point causes a feedback loop between the two bodies; a jet flow impinges on the FP, the effect of which propagates upstream where the jet impinges on the FP, and the aerodynamic and aerothermodynamic loads reach their maxima. Finally, we found that the feedback loop can be destroyed by installing a fence on the FP to reduce unsteadiness of flow field.

  5. Two body and multibody interaction in a cold Rydberg gas

    NASA Astrophysics Data System (ADS)

    Han, Jianing; Gallagher, Tom

    2009-05-01

    Cold Rydberg atoms trapped in a Magneto Optical Trap (MOT) are not isolated and they tend to bond through dipole-dipole and multiple-multiple interactions between Rydberg atoms. The dipole-dipole interaction and van der Waals interaction between two atoms have been intensively studied. However, the fact that the dipole-dipole interaction and van der Waals interaction show the same size of broadening, studied by Raithel's group, and there is transition between two molecular states, studied by Farooqi and Overstreet, can not be explained by the two atom picture. The purpose of this paper is to show the multibody nature of a dense cold Rydberg gas by studying the molecular state microwave spectrum. Specifically, single body, two body and three body interaction regions are separated. Moreover, the multibody energy levels for selected geometries are calculated. In addition, multibody blockade will be discussed. [3pt] [1] A. Reinhard, K. C. Younge, T. Cubel Liebisch, B. Knuffman, P. R. Berman, and G. Raithel, Phys. Rev. Lett. 100, 233201 (2008).[0pt] [2] S.M. Farooqi, D. Tong, S. Krishnan, J. Stanojevic,Y.P. Zhang, J.R. Ensher, A.S. Estrin, C. Boisseau, R. Cote, E.E. Eyler, and P.L. Gould, Phys. Rev. Lett. 91, 183002 (2003).[0pt] [3] K. Richard Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. A 76, 011403 (2007).

  6. Implicit Theories of Static Interactions between Two Bodies

    ERIC Educational Resources Information Center

    Montanero, M.; Suero, M. I.; Perez, A. L.; Pardo, P. J.

    2002-01-01

    There are many spontaneous conceptions related to the principle of action and reaction for two bodies in static contact. A study of a broad sample of students showed Newton's third law to be a great unknown for most of them. The conceptions were found to be consistent, forming authentic minitheories (implicit theories) with general laws governing…

  7. Proton-neutron interacting boson model under random two-body interactions

    SciTech Connect

    Yoshida, N.; Zhao, Y. M.; Arima, A.

    2009-12-15

    The low-lying states of sd-boson systems in the presence of random two-body interactions are studied in the proton-neutron interacting boson model (IBM-2). The predominance of spin-zero ground states is confirmed, and a very prominent maximum F-spin dominance in ground states is found. It turns out that the requirement of random interactions with F-spin conservation intensifies the above predominance. Collective motion in the low-lying states is discussed.

  8. Relationships between three-body and two-body interactions in fluids and solids.

    PubMed

    Wang, Liping; Sadus, Richard J

    2006-10-14

    Molecular dynamics data are reported for two-body and three-body interactions in noble gases at densities covering the gas, liquid, and solid phases. The data indicate that simple relationships exist between three- and two-body interactions in both fluid and solid phases. The relationship for liquids has a simple density dependence with only one external parameter. In contrast, the solid phase relationship depends both on density and on the square of density and requires the evaluation of two parameters. The relationships are tested for both system-size and temperature dependences. The values of the relationship parameters are only sensitive to system size when a small number of atoms are involved. For 500 or more atoms, they remain nearly constant. The relationships are valid for both subcritical and slightly supercritical temperatures. A practical benefit of the relationships is that they enable the use of two-body intermolecular potentials for the prediction of the properties of real systems without the computational expense of three-body calculations. PMID:17042611

  9. Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions

    NASA Astrophysics Data System (ADS)

    Chereji, Răzvan V.; Tolkunov, Denis; Locke, George; Morozov, Alexandre V.

    2011-05-01

    One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes into regular chromatin fibers if their rotational setting (defined by the DNA helical twist) is conserved. We describe nucleosome positions along the fiber using a thermodynamic model of finite-size particles with both intrinsic histone-DNA interactions and an effective two-body potential. We infer one- and two-body energies directly from high-throughput maps of nucleosome positions. We show that higher-order chromatin structure helps explains in vitro and in vivo nucleosome ordering in transcribed regions, and plays a leading role in establishing well-known 10-11 bp genome-wide periodicity of nucleosome positions.

  10. Collectivity of low-lying states under random two-body interactions

    SciTech Connect

    Zhao, Y. M.; Ping, J. L.; Arima, A.

    2007-11-15

    In this article we study the behavior of collectivity under random two-body interactions in the framework of the fermion dynamical symmetry model (FDSM). We found that a Hamiltonian with the SO(8) symmetry of the FDSM does not give vibrational and rotational modes under random interactions while a Hamiltonian with the SP(6) symmetry does. It is suggested that collective motions such as vibration and rotation are closely related not only to the quadruple-quadruple correlation in the Hamiltonian but also to the dynamical symmetries of the Hamiltonian.

  11. New puzzle for many-body systems with random two-body interactions

    SciTech Connect

    Johnson, Calvin W.; Nam, Hai Ah

    2007-04-15

    We continue a series of numerical experiments on many-body systems with random two-body interactions, by examining correlations in ratios in excitation energies of yrast J=0,2,4,6,8 states. Previous studies, limited only to J=0,2,4 states, had shown strong correlations in boson systems but not fermion systems. By including J{>=}6 states and considering different scatter plots, strong correlations between ratios of yrast excitation energies appear in both boson and fermion systems. Such correlations agree with real nuclear data and include the well-known limits of seniority, vibrations, and rotations.

  12. Renormalization group analysis of ultracold Fermi gases with two-body attractive interaction

    NASA Astrophysics Data System (ADS)

    Guo, Xiaoyong; Chi, Zimeng; Zheng, Qiang; Wang, Zaijun

    2016-01-01

    We propose a new functional renormalization group (RG) strategy to investigate the many-body physics of interacting ultracold Fermi gases. By mapping the Ginzburg-Landau (GL) action of Fermi gases onto a complex φ4-model, we can obtain the closed flow equation in the one-loop approximation. An analysis of the emerging RG flow gives the ground state behavior. The Hamiltonian of a Fermi gas with a two-body attractive interaction is used as a demonstration to clarify our treatment. The fixed point structure reveals not only the condensation phase transition, but also the Bardeen-Cooper-Schrieffer (BCS) to Bose-Einstein condensation (BEC) crossover. The effect of the imaginary time renormalization is also discussed. It is shown that for the dynamical field configuration our RG procedure can reproduce the well known theoretical results of BCS-BEC crossover, while under a static approximation the phase transition takes place at a higher critical temperature.

  13. One-Dimensional Traps, Two-Body Interactions, Few-Body Symmetries. II. N Particles

    NASA Astrophysics Data System (ADS)

    Harshman, N. L.

    2016-01-01

    This is the second in a pair of articles that classify the configuration space and kinematic symmetry groups for N identical particles in one-dimensional traps experiencing Galilean-invariant two-body interactions. These symmetries explain degeneracies in the few-body spectrum and demonstrate how tuning the trap shape and the particle interactions can manipulate these degeneracies. The additional symmetries that emerge in the non-interacting limit and in the unitary limit of an infinitely strong contact interaction are sufficient to algebraically solve for the spectrum and degeneracy in terms of the one-particle observables. Symmetry also determines the degree to which the algebraic expressions for energy level shifts by weak interactions or nearly-unitary interactions are universal, i.e. independent of trap shape and details of the interaction. Identical fermions and bosons with and without spin are considered. This article analyzes the symmetries of N particles in asymmetric, symmetric, and harmonic traps; the prequel article treats the one, two and three particle cases.

  14. The role of two body interaction on the broadening of a Förster resonance

    NASA Astrophysics Data System (ADS)

    Kondo, Jorge; Goncalves, Luis; Tallant, Jonathan; Booth, Donald; Shaffer, James; Marcassa, Luis

    2015-05-01

    Since the early days of ultracold Rydberg atom physics, many-body effects in ultracold trapped alkali gases has been of central interest. The first experiments in this field involved the study of Förster resonances as a function of atomic density. We present a study of a dc electric field tuned Förster resonance involving 37D state Rb atoms in a high density atomic sample held in an optical dipole trap. Our results show that as the atomic density increases, the resonance linewidth increases until the resonance peaks merge. Simultaneously, we measure the 39P state population which is produced through interactions between 37D atoms. It is shown that the 39P population depends quadratically on the total Rydberg 37D atomic population. A theoretical model that takes into account the multilevel character of the interaction and Rydberg atom blockade process using only pair interactions was implemented to explain the results. The comparison between the experimental data and the model is very good, suggesting that the Föster resonance process is dominate by two-body interaction. This work was supported by Fapesp, NSF and INCT-IQ.

  15. The two-body interaction potential in the STF tensor formalism: an application to binary asteroids

    NASA Astrophysics Data System (ADS)

    Compère, A.; Lemaître, A.

    2014-08-01

    The symmetric trace free (STF) tensor formalism, developed by Hartmann et al. (Celest Mech Dyn Astron 60:139-159. doi: 10.1007/BF00693097, 1994), is a nice tool, not much used in Celestial Mechanics. It is fully equivalent to the usual spherical harmonics but permits more elegant and compact formulations. The coupling between the gravitational fields of extended bodies with this formalism has been used in Mathis and Le Poncin-Lafitte (Astron Astrophys 497:889-910. doi: 10.1051/0004-6361/20079054, 2009) for binary stars or planetary systems, but not yet applied to binary asteroids. However, binary asteroids are common in the Solar System and usually their study requires a full two rigid body approach. The formulation of the two-body interaction potential in the STF formalism in the full two rigid body problem is detailed and completed in this article. An application to the binary asteroid (66391) 1999 KW4 is presented with a comparison of our results with other results of the literature for validation.

  16. Periodic orbit quantization of a weakly interacting two-body system using perturbed symmetry-broken trace formulas

    SciTech Connect

    Sakhr, Jamal; Whelan, Niall D.; Dumont, Randall S.

    2006-11-15

    The semiclassical limit of the quantum few-body problem has not been studied in general terms from the point of view of periodic orbit theory. In a previous paper, we studied noninteracting two-body systems [Phys. Rev. A 62, 042109 (2000)] and discussed the fact that the periodic orbits occur in continuous families. Interactions destroy the periodic orbit families leaving a discrete set of isolated periodic orbits. In this paper, we consider the effect of weak two-body interactions, which can be thought of as symmetry-breaking perturbations and can thus be analyzed using a theory developed by Creagh [Ann. Phys. (N.Y.) 248, 1 (1996)]. The Poeschl-Teller two-body system confined in a square well is analyzed to illustrate the use of the formalism. It is shown that the effect of the interaction can be evaluated for all two-particle periodic orbits, and that the coarse-grained quantum density of states can be fully reproduced from simply summing the perturbed contributions of each periodic orbit family. Good numerical estimates of the quantum singlet energies can actually be obtained, but it is found that that perturbed trace formulas cannot reproduce the multiplet splittings predicted from quantum mechanics. Several interesting properties are observed depending on the range of the interaction and on whether the interaction is attractive or repulsive.

  17. Cornell interaction in the two-body semi-relativistic framework: The Lie algebraic approach

    NASA Astrophysics Data System (ADS)

    Panahi, H.; Zarrinkamar, S.; Baradaran, M.

    2016-02-01

    We consider an approximation to the two-body spinless Salpeter equation which is valid for the case of heavy quarks with the Cornell potential. We then replace the square of kinetic term with its nonrelativistic equivalent and obtain an equation which can be alternatively viewed as the generalization of the Schrödinger equation into the relativistic regime. In the calculations, we use the Lie algebraic approach within the framework of quasi-exact solvability. With the help of the representation theory of sl(2) , the ( n+1 -dimensional matrix equation of the problem is constructed in a quite detailed manner and thereby the quasi-exact expressions for the energy eigenvalues and the corresponding wave functions as well as the allowed values of the potential parameters are obtained.

  18. Fluid-structure interaction of two bodies in an inviscid fluid

    NASA Astrophysics Data System (ADS)

    Tchieu, A. A.; Crowdy, D.; Leonard, A.

    2010-10-01

    The interaction of two arbitrary bodies immersed in a two-dimensional inviscid fluid is investigated. Given the linear and angular velocities of the bodies, the solution of the potential flow problem with zero circulation around both bodies is reduced to the determination of a suitable Laurent series in a conformally mapped domain that satisfies the boundary conditions. The potential flow solution is then used to determine the force and moment acting on each body by using generalized Blasius formulas. The current formulation is applied to two examples. First, the case of two rigid circular cylinders interacting in an unbounded domain is investigated. The forces on two cylinders with prescribed motion (forced-forced) is determined and compared to previous results for validation purposes. We then study the response of a single "free" cylinder due to the prescribed motion of the other cylinder (forced-free). This forced-free situation is used to justify the hydrodynamic benefits of drafting in aquatic locomotion. In the case of two neutrally buoyant circular cylinders, the aft cylinder is capable of attaining a substantial propulsive force that is the same order of magnitude of its inertial forces. Additionally, the coupled interaction of two cylinders given an arbitrary initial condition (free-free) is studied to show the differences of perfect collisions with and without the presence of an inviscid fluid. For a certain range of collision parameters, the fluid acts to deflect the cylinder paths just enough before the collision to drastically affect the long time trajectories of the bodies. In the second example, the flapping of two plates is explored. It is seen that the interactions between each plate can cause a net force and torque at certain instants in time, but for idealized sinusoidal motions in irrotational potential flow, there is no net force and torque acting at the system center.

  19. Interacting quantum walkers: two-body bosonic and fermionic bound states

    NASA Astrophysics Data System (ADS)

    Krapivsky, P. L.; Luck, J. M.; Mallick, K.

    2015-11-01

    We investigate the dynamics of bound states of two interacting particles, either bosons or fermions, performing a continuous-time quantum walk on a one-dimensional lattice. We consider the situation where the distance between both particles has a hard bound, and the richer situation where the particles are bound by a smooth confining potential. The main emphasis is on the velocity characterizing the ballistic spreading of these bound states, and on the structure of the asymptotic distribution profile of their center-of-mass coordinate. The latter profile generically exhibits many internal fronts.

  20. Solution of two-body relativistic bound state equations with confining plus Coulomb interactions

    NASA Technical Reports Server (NTRS)

    Maung, Khin Maung; Kahana, David E.; Norbury, John W.

    1992-01-01

    Studies of meson spectroscopy have often employed a nonrelativistic Coulomb plus Linear Confining potential in position space. However, because the quarks in mesons move at an appreciable fraction of the speed of light, it is necessary to use a relativistic treatment of the bound state problem. Such a treatment is most easily carried out in momentum space. However, the position space Linear and Coulomb potentials lead to singular kernels in momentum space. Using a subtraction procedure we show how to remove these singularities exactly and thereby solve the Schroedinger equation in momentum space for all partial waves. Furthermore, we generalize the Linear and Coulomb potentials to relativistic kernels in four dimensional momentum space. Again we use a subtraction procedure to remove the relativistic singularities exactly for all partial waves. This enables us to solve three dimensional reductions of the Bethe-Salpeter equation. We solve six such equations for Coulomb plus Confining interactions for all partial waves.

  1. One-Dimensional Traps, Two-Body Interactions, Few-Body Symmetries: I. One, Two, and Three Particles

    NASA Astrophysics Data System (ADS)

    Harshman, N. L.

    2016-01-01

    This is the first in a pair of articles that classify the configuration space and kinematic symmetry groups for N identical particles in one-dimensional traps experiencing Galilean-invariant two-body interactions. These symmetries explain degeneracies in the few-body spectrum and demonstrate how tuning the trap shape and the particle interactions can manipulate these degeneracies. The additional symmetries that emerge in the non-interacting limit and in the unitary limit of an infinitely strong contact interaction are sufficient to algebraically solve for the spectrum and degeneracy in terms of the one-particle observables. Symmetry also determines the degree to which the algebraic expressions for energy level shifts by weak interactions or nearly-unitary interactions are universal, i.e. independent of trap shape and details of the interaction. Identical fermions and bosons with and without spin are considered. This article sequentially analyzes the symmetries of one, two and three particles in asymmetric, symmetric, and harmonic traps; the sequel article treats the N particle case.

  2. Repulsive bound-atom pairs in an optical lattice with two-body interaction of nearest neighbors

    SciTech Connect

    Wang, Y.-M.; Liang, J.-Q.

    2010-04-15

    Repulsively interacting particles in a periodic potential can form bound composite objects with long lifetimes, as has been observed experimentally [Winkler et al., Nature (London) 441, 853 (2006)]. In this paper, a complete two-particle solution of one-dimensional periodical potential was derived in a strong interaction regime, where the on-site approximation of a two-body interaction in the Bose-Hubbard model (BHM) is extended to include the interaction of nearest neighbors, which results in atom-pair hopping. The energy spectrum of the bound pair is drastically reshaped due to the pair-hopping term, and complex eigenenergy corresponding to metastable states is also found that has not been discovered in the usual BHM. When the absolute value of a center-of-mass quasimomentum wave vector is greater than a critical value (|K|>K{sub c}), two bound-pair solutions are found. Furthermore, the spatial and momentum distributions of the bound pair displays a crossover from dark to bright soliton-like solutions in the extended BHM. Our results reduce to that of the usual BHM in the weak interaction case.

  3. Effects of the two-body and three-body hyperon-nucleon interactions in Λ hypernuclei

    NASA Astrophysics Data System (ADS)

    Lonardoni, D.; Gandolfi, S.; Pederiva, F.

    2013-04-01

    Background: The calculation of the hyperon binding energy in hypernuclei is crucial to understanding the interaction between hyperons and nucleons.Purpose: We assess the relative importance of two- and three-body hyperon-nucleon force by studying the effect of the hyperon-nucleon-nucleon interaction in closed shell Λ hypernuclei from A = 5 to 91.Methods: The Λ binding energy has been calculated using the auxiliary field diffusion Monte Carlo method for the first time, to study light and heavy hypernuclei within the same model.Results: Our results show that including a three-body component in the hyperon-nucleon interaction leads to a saturation of the Λ binding energy remarkably close to the experimental data. In contrast, the two-body force alone gives an unphysical limit for the binding energy.Conclusions: The repulsive contribution of the three-body hyperon-nucleon-nucleon force is essential to reproduce, even qualitatively, the binding energy of hypernuclei in the mass range considered.

  4. Topological quantum-phase coherence in full counting statistics of transport electrons with two-body interaction

    NASA Astrophysics Data System (ADS)

    Guo, Xiao-Fang; Xue, Hai-Bin; Liang, Jiu-Qing

    2014-08-01

    The full counting statistics of electron transport through two parallel quantum dots with antiparallel magnetic fluxes is investigated as a probe to detect the topological quantum-phase coherence (TQPC), which results in the characteristic oscillation of the zero-frequency cumulants including the shot noise and skewness. We show explicitly the phase transition of cumulant spectrum-patterns induced by the topology change of electron path-loops while the pattern period, which depends only on the topology (or Chern number), is robust against the variation of Coulomb interaction and interdot coupling strengths. Most importantly we report for the first time on a new type of TQPC, which is generated by the two-particle interaction and does not exist in the single-particle wave function interference. Moreover, the accurately quantized peaks of Fano-factor spectrum, which characterize the super- and sub-Poissonian shot noises, are of fundamental importance in technical applications similar to the superconducting quantum interference device.

  5. Gravitational self-force corrections to two-body tidal interactions and the effective one-body formalism

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Damour, Thibault

    2014-12-01

    Tidal interactions have a significant influence on the late dynamics of compact binary systems, which constitute the prime targets of the upcoming network of gravitational-wave detectors. We refine the theoretical description of tidal interactions (hitherto known only to the second post-Newtonian level) by extending our recently developed analytic self-force formalism, for extreme-mass-ratio binary systems, to the computation of several tidal invariants. Specifically, we compute, to linear order in the mass ratio and to the 7.5th post-Newtonian order, the following tidal invariants: the square and the cube of the gravitoelectric quadrupolar tidal tensor, the square of the gravitomagnetic quadrupolar tidal tensor, and the square of the gravitoelectric octupolar tidal tensor. Our high-accuracy analytic results are compared to recent numerical self-force tidal data by Dolan et al. [arXiv:1406.4890 [Phys. Rev. D (to be published)] ], and, notably, provide an analytic understanding of the light ring asymptotic behavior found by them. We transcribe our kinematical tidal-invariant results in the more dynamically significant effective one-body description of the tidal interaction energy. By combining, in a synergetic manner, analytical and numerical results, we provide simple, accurate analytic representations of the global, strong-field behavior of the gravitoelectric quadrupolar tidal factor. A striking finding is that the linear-in-mass-ratio piece in the latter tidal factor changes sign in the strong-field domain, to become negative (while its previously known second post-Newtonian approximant was always positive). We, however, argue that this will be more than compensated by a probable fast growth, in the strong-field domain, of the nonlinear-in-mass-ratio contributions in the tidal factor.

  6. Analytic determination of the eight-and-a-half post-Newtonian self-force contributions to the two-body gravitational interaction potential

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Damour, Thibault

    2014-05-01

    We analytically compute, to the eight-and-a-half post-Newtonian order, and to linear order in the mass ratio, the radial potential describing (within the effective one-body formalism) the gravitational interaction of two bodies, thereby extending previous analytic results. These results are obtained by applying analytical gravitational self-force theory (for a particle in circular orbit around a Schwarzschild black hole) to Detweiler's gauge-invariant redshift variable. We emphasize the increase in "transcendentality" of the numbers entering the post-Newtonian expansion coefficients as the order increases, in particular we note the appearance of ζ(3) (as well as the square of Euler's constant γ) starting at the seventh post-Newtonian order. We study the convergence of the post-Newtonian expansion as the expansion parameter u =GM/(c2r) leaves the weak-field domain u ≪1 to enter the strong field domain u=O(1).

  7. Effect of the band structure in a rigorous two-body model with long-range interactions in 1D optical lattices

    NASA Astrophysics Data System (ADS)

    Kristensen, Tom; Simoni, Andrea; Launay, Jean-Michel

    2016-05-01

    We compute scattering and bound state properties for two ultracold molecules in a pure 1D optical lattice. We introduce reference functions with complex quasi-momentum that naturally account for the effect of excited energy bands. Our exact results for a short-range interaction are first compared with the simplest version of the standard Bose-Hubbard (BH) model. Such comparison allows us to highlight the effect of the excited bands, of the non-on-site interaction and of tunneling with distant neighbor, that are not taken into account in the BH model. The effective interaction can depend strongly on the particle quasi-momenta and can present a resonant behavior even in a deep lattice. As a second step, we study scattering of two polar particles in the optical lattice. Peculiar Wigner threshold laws stem from the interplay of the long range dipolar interaction and the presence of the energy bands. We finally assess the validity of an extended Bose-Hubbard model for dipolar gases based on our exact two-body calculations. This work was supported by the Agence Nationale de la Recherche (Contract No. ANR-12-BS04-0020-01).

  8. Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?

    PubMed

    Ghomi, Hamed Tabatabaei; Thompson, Jared J; Lill, Markus A

    2014-10-01

    Distance-based statistical potentials have long been used to model condensed matter systems, e.g. as scoring functions in differentiating native-like protein structures from decoys. These scoring functions are based on the assumption that the total free energy of the protein can be calculated as the sum of pairwise free energy contributions derived from a statistical analysis of pair-distribution functions. However, this fundamental assumption has been challenged theoretically. In fact the free energy of a system with N particles is only exactly related to the N-body distribution function. Based on this argument coarse-grained multi-body statistical potentials have been developed to capture higher-order interactions. Having a coarse representation of the protein and using geometric contacts instead of pairwise interaction distances renders these models insufficient in modeling details of multi-body effects. In this study, we investigated if extending distance-dependent pairwise atomistic statistical potentials to corresponding interaction functions that are conditional on a third interacting body, defined as quasi-three-body statistical potentials, could model details of three-body interactions. We also tested if this approach could improve the predictive capabilities of statistical scoring functions for protein structure prediction. We analyzed the statistical dependency between two simultaneous pairwise interactions and showed that there is surprisingly little if any dependency of a third interacting site on pairwise atomistic statistical potentials. Also the protein structure prediction performance of these quasi-three-body potentials is comparable with their corresponding two-body counterparts. The scoring functions developed in this study showed better or comparable performances compared to some widely used scoring functions for protein structure prediction. PMID:25212727

  9. Energy and structural properties of N -boson clusters attached to three-body Efimov states: Two-body zero-range interactions and the role of the three-body regulator

    NASA Astrophysics Data System (ADS)

    Yan, Yangqian; Blume, D.

    2015-09-01

    The low-energy spectrum of N -boson clusters with pairwise zero-range interactions is believed to be governed by a three-body parameter. We study the ground state of N -boson clusters with infinite two-body s -wave scattering length by performing ab initio Monte Carlo simulations. To prevent Thomas collapse, different finite-range three-body regulators are used. The energy and structural properties for the three-body Hamiltonian with two-body zero-range interactions and three-body regulator are in much better agreement with the "ideal zero-range Efimov theory" results than those for Hamiltonian with two-body finite-range interactions. For larger clusters we find that the ground-state energy and structural properties of the Hamiltonian with two-body zero-range interactions and finite-range three-body regulators are not universally determined by the three-body parameter, i.e., dependencies on the specific form of the three-body regulator are observed. For comparison, we consider Hamiltonian with two-body van der Waals interactions and no three-body regulator. For the interactions considered, the ground-state energy of the N -body clusters is—if scaled by the three-body ground-state energy—fairly universal, i.e., the dependence on the short-range details of the two-body van der Waals potentials is small. Our results are compared with those in the literature.

  10. Two-Body Scattering in (1 + 1) Dimensions by a Semi-relativistic Formalism and a Hulthén Interaction Potential

    NASA Astrophysics Data System (ADS)

    Hassanabadi, S.; Ghominejad, M.; Thylwe, K.-E.

    2015-04-01

    Scattering solutions of two-body Spinless Salpeter Equation (SSE) are investigated in the center of mass frame with a repulsive, symmetric Hulthén potential in one spatial dimension. Transmission and reflection coefficients are calculated and discussed.

  11. Two- and quasi-two-body strange particle final state production in. pi. /sup +/p interactions at low to intermediate energies

    SciTech Connect

    Hanson, P.

    1982-10-01

    The two and quasi-two body final states ..sigma../sup +/K/sup +/, ..sigma../sup +/K* (892)/sup +/, ..sigma..*(1385)/sup +/K/sup +/, ..sigma..(1385)/sup +/K*(892)/sup +/ produced by neutral strangeness exchange in ..pi../sup +/p interactions are studied using our own 1-3 GeV/c data, comprising the 14 incident momenta of a two million picture bubble chamber experiment, in combination with the world data on the same and related channels. Because low energy resonance formation is not strongly coupled to the ..sigma..,..sigma..* production channels, at very modest incident momenta their dominant features are seen to be understandable in terms of high energy hypercharge exchange phenomenology. We find that Regge models fitted to data in the 10 to 20 GeV/c range adequately describe the ..sigma.. and ..sigma..* channels down to within a few hundred MeV/c of threshold and out to large center of mass scattering angles, and that over the range of the available world data weak exchange degeneracy expectations for these reactions are at least qualitatively successful. We observe that the SU(2), SU(3) flavor symmetries successfully describe these hypercharge exchange processes and relate them to charge exchange via sum rules and equalities expressing flavor independence of the strong interaction; in particular, we derive and test on the available world data a mass broken SU(3) sum rule for ..pi../sup +/p ..-->.. K/sup +/..sigma../sup +/, ..pi../sup -/p ..-->.. K/sup 0/..lambda.., K/sup -/p ..-->.. anti K/sup 0/n and test over a wider range of momenta than before an earlier expression relating ..sigma..* and ..delta.. production. We also find at least qualitative agreement between quark model predictions for forward hypercharge exchange and the data, and we find that 90/sup 0/ hypercharge exchange cross sections also conform to the expectations of the quark constituent picture for hadrons.

  12. Applications of two-body Dirac equations to the meson spectrum with three versus two covariant interactions, SU(3) mixing, and comparison to a quasipotential approach

    SciTech Connect

    Crater, Horace W.; Schiermeyer, James

    2010-11-01

    In a previous paper, Crater and Van Alstine applied the two-body Dirac equations of constraint dynamics to quark-antiquark bound states using a relativistic extention of the Adler-Piran potential and compared their spectral results to those from other approaches which also considered meson spectroscopy as a whole and not in parts. In this paper, we explore in more detail the differences and similarities in an important subset of those approaches, the quasipotential approach. In the earlier paper, the transformation properties of the quark-antiquark potentials were limited to a scalar and an electromagnetic-like four-vector, with the former accounting for the confining aspects of the overall potential, and the latter the short range portion. The static Adler-Piran potential was first given an invariant form and then apportioned between those two different types of potentials. Here, we make a change in this apportionment that leads to a substantial improvement in the resultant spectroscopy by including a timelike confining vector potential over and above the scalar confining one and the electromagnetic-like vector potential. Our fit includes 19 more mesons than the earlier results and we modify the scalar portion of the potential in such a way that allows this formalism to account for the isoscalar mesons {eta} and {eta}{sup '} not included in the previous work. Continuing the comparisons of formalisms and spectral results made in the previous paper with other approaches to meson spectroscopy, we examine in this paper the quasipotential approach of Ebert, Faustov, and Galkin.

  13. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

    NASA Astrophysics Data System (ADS)

    Wang, Yimin; Bowman, Joel M.; Kamarchik, Eugene

    2016-03-01

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na+H2O, F-H2O, and Cl-H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20 000 coupled cluster CCSD(T) energies (awCVTZ basis for Na+ and aVTZ basis for Cl- and F-), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  14. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

    PubMed

    Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs. PMID:27004880

  15. Orbits of Two-Body Problem From the Lenz Vector

    ERIC Educational Resources Information Center

    Caplan, S.; And Others

    1978-01-01

    Obtains the orbits with reference to the center of mass of two bodies under mutual universe square law interaction by use of the eccentricity vector which is equivalent to the Lenz vector within a numerical factor. (Author/SL)

  16. Towards a two-body neuroscience.

    PubMed

    Dumas, Guillaume

    2011-05-01

    Recent work from our interdisciplinary research group has revealed the emergence of inter-brain synchronization across multiple frequency bands during social interaction.1 Our findings result from the close collaboration between experts who study neural dynamics and developmental psychology. The initial aim of the collaboration was to combine knowledge from these two fields in order to move from a classical one-brain neuroscience towards a novel two-body approach. A new technique called hyperscanning has made it possible to study the neural activity of two individuals simultaneously. However, this advanced methodology was not sufficient in itself. What remained to be found was a way to promote real-time reciprocal social interaction between two individuals during brain recording and analyze the neural and behavioral phenomenon from an inter-individual perspective. Approaches used in infancy research to study nonverbal communication and coordination, between a mother and her child for example, have so far been poorly applied to neuroimaging experiments. We thus adapted an ecological two-body experiment inspired by the use of spontaneous imitation in preverbal infants. Numerous methodological and theoretical problems had to be overcome, ranging from the choice of a common time-unit for behavioral and brain recordings to the creation of algorithms for data processing between distant brain regions in different brains. This article will discuss the underlying issues and perspectives involved in elucidating the pathway from individual to social theories of cognition. PMID:21980578

  17. Towards a two-body neuroscience

    PubMed Central

    2011-01-01

    Recent work from our interdisciplinary research group has revealed the emergence of inter-brain synchronization across multiple frequency bands during social interaction.1 Our findings result from the close collaboration between experts who study neural dynamics and developmental psychology. The initial aim of the collaboration was to combine knowledge from these two fields in order to move from a classical one-brain neuroscience towards a novel two-body approach. A new technique called hyperscanning has made it possible to study the neural activity of two individuals simultaneously. However, this advanced methodology was not sufficient in itself. What remained to be found was a way to promote real-time reciprocal social interaction between two individuals during brain recording and analyze the neural and behavioral phenomenon from an inter-individual perspective. Approaches used in infancy research to study nonverbal communication and coordination, between a mother and her child for example, have so far been poorly applied to neuroimaging experiments. We thus adapted an ecological two-body experiment inspired by the use of spontaneous imitation in preverbal infants. Numerous methodological and theoretical problems had to be overcome, ranging from the choice of a common time-unit for behavioral and brain recordings to the creation of algorithms for data processing between distant brain regions in different brains. This article will discuss the underlying issues and perspectives involved in elucidating the pathway from individual to social theories of cognition. PMID:21980578

  18. Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions.

    PubMed

    Parker, Andrew S; Griswold, Karl E; Bailey-Kellogg, Chris

    2011-04-01

    Exogenous enzymes, signaling peptides, and other classes of nonhuman proteins represent a potentially massive but largely untapped pool of biotherapeutic agents. Adapting a foreign protein for therapeutic use poses numerous design challenges. We focus here on one significant problem: modifying the protein to mitigate the immune response mounted against "non-self" proteins, while not adversely affecting the protein's stability or therapeutic activity. In order to propose such variants suitable for experimental evaluation, this paper develops a computational method to select sets of mutations predicted to delete immunogenic T-cell epitopes, as evaluated by a 9-mer potential, while simultaneously maintaining important residues and residue interactions, as evaluated by one- and two-body potentials. While this design problem is NP-hard, we develop an integer programming approach that works very well in practice. We demonstrate the effectiveness of our approach by developing plans for biotherapeutic proteins that, in previous studies, have been partially deimmunized via extensive experimental characterization and modification of limited segments. In contrast, our global optimization technique considers an entire protein and accounts for all residues, residue interactions, and epitopes in proposing candidates worth subjecting to experimental evaluation. PMID:21523929

  19. Two-body problem in graphene

    NASA Astrophysics Data System (ADS)

    Kezerashvili, Roman Ya.; Berman, Oleg L.; Ziegler, Klaus

    2013-04-01

    The description of excitons in graphene as a bound electron and hole using two dimensional Dirac equation is presented. We introduce a transformation to decouple the center-of-mass motion and the relative motion and analyze the two body problem with action-at-a-distance inter-particle Coulomb potential in a gapped graphene sheet. Then turn to a problem of two Dirac particles in two-layer graphene sheets separated by a dielectric, assuming that exciton in this system is formed by the electron located in the one graphene sheet and the hole located in the other. Assuming that interaction potential and both relative and center-of-mass kinetic energies are small compared to the gap energy, the analytical solution for the wave functions and energy spectrum of the exciton are found. The advantage of the consideration of exciton formed by an electron and a hole from two different graphene layers, separated by an insulating slab, is that the dielectric slab creates the barrier for the electron-hole recombination which increases the life-time of the exciton compared to the exciton formed by an electron and a hole in a single graphene layer.

  20. Two-body nonleptonic decays of D mesons

    NASA Astrophysics Data System (ADS)

    Buccella, F.; Lusignoli, M.; Miele, G.; Pugliese, A.

    1992-06-01

    The amplitudes for two-body Cabibbo allowed nonleptonic decays of D mesons are evaluated within the factorization approximation from the effective Hamiltonian including short distance QCD corrections to next-to-leading order. Annihilation and W-exchange contributions as well as final state interaction effects have been included and are in fact crucial to obtain agreement with the experimental data.

  1. Bioinformatic prediction and in vivo validation of residue-residue interactions in human proteins

    NASA Astrophysics Data System (ADS)

    Jordan, Daniel; Davis, Erica; Katsanis, Nicholas; Sunyaev, Shamil

    2014-03-01

    Identifying residue-residue interactions in protein molecules is important for understanding both protein structure and function in the context of evolutionary dynamics and medical genetics. Such interactions can be difficult to predict using existing empirical or physical potentials, especially when residues are far from each other in sequence space. Using a multiple sequence alignment of 46 diverse vertebrate species we explore the space of allowed sequences for orthologous protein families. Amino acid changes that are known to damage protein function allow us to identify specific changes that are likely to have interacting partners. We fit the parameters of the continuous-time Markov process used in the alignment to conclude that these interactions are primarily pairwise, rather than higher order. Candidates for sites under pairwise epistasis are predicted, which can then be tested by experiment. We report the results of an initial round of in vivo experiments in a zebrafish model that verify the presence of multiple pairwise interactions predicted by our model. These experimentally validated interactions are novel, distant in sequence, and are not readily explained by known biochemical or biophysical features.

  2. Computational learning on specificity-determining residue-nucleotide interactions

    PubMed Central

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Moses, Alan M.; Zhang, Zhaolei

    2015-01-01

    The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein–DNA interactions across different DNA binding families. PMID:26527718

  3. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    SciTech Connect

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  4. Terminal residue hydrophobicity modulates transmembrane helix-helix interactions.

    PubMed

    Ng, Derek P; Deber, Charles M

    2014-06-17

    Central to the formation of tertiary structure in membrane protein folding is the presence of amino acid sequence motifs (such as "small-XXX-small" segments) in the TM segments that promote interaction-compatible surfaces through which the TM α-helices interact. Here, we sought to elucidate additional factors that may work in tandem to dictate the ultimate interaction fate of TM-embedded segments. In this context, we used proteolipid protein (PLP), the major protein from central nervous system myelin for which mutant-dependent non-native oligomerization has been implicated in neurological disorders, to explore the specific effects of TM boundary residues (the membrane entry and exit points), keying on the secondary structure and self-association of peptides corresponding to the PLP TM2 α-helix (wild-type sequence ⁶⁶AFQYVIYGTASFFFLYGALLLAEGF⁹⁰). Using gel electrophoresis, circular dichroism, and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate (SDS), we found that mutation of F90 to residues such as A, I, L, or V maintains the onset of TM2-TM2 dimerization, whereas mutation to E, G, Q, N, S, or T abrogates dimer formation. We attribute this sensitivity to changes in local hydrophobicity, viz., a decrease in hydrophobicity reduces local lipid-peptide interactions, which in turn disrupts peptide α-helicity and hence the effectiveness of an incipient interaction-compatible surface. Our results show that the secondary structure and oligomeric state of PLP TM2 Lys-tagged peptides are significantly modulated by the specific nature of their C-terminal boundary residue, thus providing insight as to how point mutations, particularly where they produce disease states, can compromise the folding process. PMID:24857611

  5. Two-body nonleptonic decays of D mesons

    NASA Astrophysics Data System (ADS)

    Buccella, F.; Lusignoli, M.; Miele, G.; Pugliese, A.

    1992-01-01

    The amplitudes for two body Cabibbo allowed nonleptonic decays of D mesons are evaluated. The factorization approximation from the effective hamiltonian including short distance corrections to next to leading order are considered. Annihilation and W exchange contributions as well as final state interaction effects are crucial to obtain agreement with the experimental data. The decay amplitudes in the factorized approximation are given. The matrix elements of currents for c decay and annihilation terms are discussed. The model used to introduce final state interaction effects is described. The results and conclusions are presented. A discussion of decays to VV final states is given.

  6. Controller-structure interaction compensation using adaptive residual mode filters

    NASA Technical Reports Server (NTRS)

    Davidson, Roger A.; Balas, Mark J.

    1990-01-01

    It is not feasible to construct controllers for large space structures or large scale systems (LSS's) which are of the same order as the structures. The complexity of the dynamics of these systems is such that full knowledge of its behavior cannot by processed by today's controller design methods. The controller for system performance of such a system is therefore based on a much smaller reduced-order model (ROM). Unfortunately, the interaction between the LSS and the ROM-based controller can produce instabilities in the closed-loop system due to the unmodeled dynamics of the LSS. Residual mode filters (RMF's) allow the systematic removal of these instabilities in a matter which does not require a redesign of the controller. In addition RMF's have a strong theoretical basis. As simple first- or second-order filters, the RMF CSI compensation technique is at once modular, simple and highly effective. RMF compensation requires knowledge of the dynamics of the system modes which resulted in the previous closed-loop instabilities (the residual modes), but this information is sometimes known imperfectly. An adaptive, self-tuning RMF design, which compensates for uncertainty in the frequency of the residual mode, has been simulated using continuous-time and discrete-time models of a flexible robot manipulator. Work has also been completed on the discrete-time experimental implementation on the Martin Marietta flexible robot manipulator experiment. This paper will present the results of that work on adaptive, self-tuning RMF's, and will clearly show the advantage of this adaptive compensation technique for controller-structure interaction (CSI) instabilities in actively-controlled LSS's.

  7. Two-body bound states & the Bethe-Salpeter equation

    SciTech Connect

    Pichowsky, M.; Kennedy, M.; Strickland, M.

    1995-01-18

    The Bethe-Salpeter formalism is used to study two-body bound states within a scalar theory: two scalar fields interacting via the exchange of a third massless scalar field. The Schwinger-Dyson equation is derived using functional and diagrammatic techniques, and the Bethe-Salpeter equation is obtained in an analogous way, showing it to be a two-particle generalization of the Schwinger-Dyson equation. The authors also present a numerical method for solving the Bethe-Salpeter equation without three-dimensional reduction. The ground and first excited state masses and wavefunctions are computed within the ladder approximation and space-like form factors are calculated.

  8. Loschmidt echoes in two-body random matrix ensembles

    NASA Astrophysics Data System (ADS)

    Pižorn, Iztok; Prosen, Tomaž; Seligman, Thomas H.

    2007-07-01

    Fidelity decay is studied for quantum many-body systems with a dominant independent particle Hamiltonian resulting, e.g., from a mean field theory with a weak two-body interaction. The diagonal terms of the interaction are included in the unperturbed Hamiltonian, while the off-diagonal terms constitute the perturbation that distorts the echo. We give the linear response solution for this problem in a random matrix framework. While the ensemble average shows no surprising behavior, we find that the typical ensemble member as represented by the median displays a very slow fidelity decay known as “freeze.” Numerical calculations confirm this result and show that the ground state even on average displays the freeze. This may contribute to explanation of the “unreasonable” success of mean field theories.

  9. Mutation analysis of the Pip interaction domain reveals critical residues for protein–protein interactions

    PubMed Central

    Ortiz, Maria Antonia; Light, James; Maki, Richard A.; Assa-Munt, Nuria

    1999-01-01

    The PU.1 interaction partner (Pip) is a member of the interferon regulatory factor family that regulates gene expression through heterodimerization with the ETS transcription factor PU.1. Binding of Pip alone to DNA is weak, and usually it is recruited by phosphorylated PU.1 to form a strong ternary complex with specific DNA sequences. An approach combining sequence homology analysis, secondary structure predictions, and a precise mutational strategy has been used to determine critical residues within the Pip heterodimerization domain that contribute to ternary complex formation. We have delimited the Pip interaction domain to residues 245–422 by using deletion analysis. Site-directed mutagenesis of conserved polar amino acids within two predicted α-helices contained in this region, and which are highly conserved in the IRF family, confirmed the importance of these residues for Pip–PU.1 interaction with DNA as well as for trans-activation activity. Our results suggest the existence of a functional epitope essential for heterodimerization between Pip and PU.1 and possibly, in general, between interferon regulatory factor family members and their partners. PMID:10077581

  10. Interactions between the transmembrane domains of CD39: identification of interacting residues by yeast selection

    PubMed Central

    Paavilainen, Sari; Guidotti, Guido

    2015-01-01

    Rat CD39, a membrane-bound ectonucleoside triphosphate diphosphohydrolase that hydrolyzes extracellular nucleoside tri- and diphosphates, is anchored to the membrane by two transmembrane domains at the two ends of the molecule. The transmembrane domains are important for enzymatic activity, as mutants lacking one or both of these domains have a fraction of the enzymatic activity of the wild-type CD39. We investigated the interactions between the transmembrane domains by using a strain of yeast that requires surface expression of CD39 for growth. Random mutagenesis of selected amino acid residues in the N-terminal transmembrane domain revealed that the presence of charged amino acids at these positions prevents expression of functional protein. Rescue of the growth of these mutants by complementary mutations on selected residues of the C-terminal transmembrane domain indicates that there is contact between particular faces of the transmembrane domains. PMID:26258004

  11. Ultralow field magnetization reversal of two-body magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Li, Fei; Lu, Jincheng; Lu, Xiaofeng; Tang, Rujun; Sun, Z. Z.

    2016-08-01

    Field induced magnetization reversal was investigated in a system of two magnetic nanoparticles with uniaxial anisotropies and magnetostatic interaction. By using the micromagnetic simulation, ultralow switching field strength was found when the separation distance between the two particles reaches a critical small value (on nanometer scale) in the perpendicular configuration where the anisotropic axes of the two particles are perpendicular to the separation line. The switching field increases sharply when the separation is away from the critical distance. The ultralow field switching phenomenon was missed in the parallel configuration where both the anisotropic axes are aligned along the separation line of the two particles. The micromagnetic results are consistent with the previous theoretical prediction [J. Appl. Phys. 109, 104303 (2011)] where dipolar interaction between two single-domain magnetic particles was considered. Our present simulations offered further proofs and possibilities for the low-power applications of information storage as the two-body magnetic nanoparticles might be implemented as a composite information bit.

  12. The study of the role of the two-body force in determining level densities

    NASA Astrophysics Data System (ADS)

    Huang, Po-Lin

    The study of the role of the two-body force in determining level densities explored the characteristics of the two-body force and their impact on nuclear level densities. Two different theoretical approaches, the statistical mechanical model and moment expansion method, were used for the determining the impact of the two-body force on level densities. Discrete levels in the lower excitation region were compiled to provide information about level density systematics. A shell model calculation for a number of light nuclei allowed a test of the input parameters including single particle energies and two-body matrix elements. Generally good agreement was found between the calculated and observed energies of low-lying states. A comparison of the results obtained with three widely used interactions for nuclei with mass numbers 18 and 20 allowed some insight into the two-body interaction and the possibilities for improving it. For the level density calculations twenty four nuclei with mass numbers between 20 and 41 were used. Both the values from tabulations of low-lying levels and the results from previous studies of level densities at 7 Mev and at 20 Mev were included. It was found that the parameters derived from the higher energy measurements gave poor results at energies below 5 Mev. The discrepancies appeared to be related to problems in determining one of the two parameters involved. Two approaches were used in an effort to improve the precision of this parameter. Both were reasonably successful. Calculations of the level of density using a super conducting model within a statistical mechanical framework and a full two-body interaction utilizing a moment method approach were completed. Both gave a reasonably good representation of the data. An examination of the significance of the analysis for future study of the two body force and of nuclear level densities is presented.

  13. Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

    PubMed Central

    Ahmad, Shandar; Mizuguchi, Kenji

    2011-01-01

    Computational prediction of residues that participate in protein-protein interactions is a difficult task, and state of the art methods have shown only limited success in this arena. One possible problem with these methods is that they try to predict interacting residues without incorporating information about the partner protein, although it is unclear how much partner information could enhance prediction performance. To address this issue, the two following comparisons are of crucial significance: (a) comparison between the predictability of inter-protein residue pairs, i.e., predicting exactly which residue pairs interact with each other given two protein sequences; this can be achieved by either combining conventional single-protein predictions or making predictions using a new model trained directly on the residue pairs, and the performance of these two approaches may be compared: (b) comparison between the predictability of the interacting residues in a single protein (irrespective of the partner residue or protein) from conventional methods and predictions converted from the pair-wise trained model. Using these two streams of training and validation procedures and employing similar two-stage neural networks, we showed that the models trained on pair-wise contacts outperformed the partner-unaware models in predicting both interacting pairs and interacting single-protein residues. Prediction performance decreased with the size of the conformational change upon complex formation; this trend is similar to docking, even though no structural information was used in our prediction. An example application that predicts two partner-specific interfaces of a protein was shown to be effective, highlighting the potential of the proposed approach. Finally, a preliminary attempt was made to score docking decoy poses using prediction of interacting residue pairs; this analysis produced an encouraging result. PMID:22194998

  14. The Sharma-Parthasarathy stochastic two-body problem

    SciTech Connect

    Cresson, J.

    2015-03-15

    We study the Sharma-Parthasarathy stochastic two-body problem introduced by Sharma and Parthasarathy in [“Dynamics of a stochastically perturbed two-body problem,” Proc. R. Soc. A 463, 979-1003 (2007)]. In particular, we focus on the preservation of some fundamental features of the classical two-body problem like the Hamiltonian structure and first integrals in the stochastic case. Numerical simulations are performed which illustrate the dynamical behaviour of the osculating elements as the semi-major axis, the eccentricity, and the pericenter. We also derive a stochastic version of Gauss’s equations in the planar case.

  15. Description and evaluation of nuclear masses based on residual proton-neutron interactions

    SciTech Connect

    Fu, G. J.; Lei, Y.; Jiang, H.; Zhao, Y. M.; Sun, B.; Arima, A.

    2011-09-15

    In this paper we study the residual proton-neutron interactions and make use of the systematics of these interactions to describe experimental data of nuclear masses and to predict some of the unknown masses. The odd-even effect staggering of the residual proton-neutron interaction between the last proton and the last neutron is found and argued in terms of pairing interactions. Two local mass relations, which work very accurately for masses of four neighboring nuclei, are discovered. The accuracy of our predicted masses for medium and heavy nuclei is competitive with that of the AME2003 extrapolations, with the virtue of simplicity.

  16. Exactness of wave functions from two-body exponential transformations in many-body quantum theory

    SciTech Connect

    Mazziotti, David A.

    2004-01-01

    Recent studies have considered the possibility that the exact ground-state wavefunction from any Hamiltonian with two-particle interactions may be generated from a single finite two-body exponential transformation acting on an arbitrary Slater determinant [Piecuch et al., Phys. Rev. Lett. 90, 113001 (2003)]. Using the Campbell-Baker-Hausdorff relation, we show that it is difficult for the variational minimum of this trial wave function to satisfy the contracted Schroedinger equation which is a necessary and sufficient condition for the wave function to satisfy the Schroedinger equation. A counterexample is presented through the Lipkin quasispin model with 4-50 fermions. When the number of fermions exceeds four, the wave function from a finite two-body exponential transformation is shown to be inexact. If the trial wave function ansatz is extended to include products of finite two-body exponential transformations acting on an arbitrary Slater-determinant reference, then we show that the ansatz includes the exact ground-state wave function from any Hamiltonian with only two-particle interactions. Connections between the two-body exponential transformation of the wave function and recent research on two-body exponential similarity transformations of the Hamiltonian [S.R. White, J. Chem. Phys. 117, 7472 (2002)] are discussed.

  17. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    PubMed

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. PMID:25311860

  18. Two-component Bose gases with one-body and two-body couplings

    NASA Astrophysics Data System (ADS)

    Lellouch, Samuel; Dao, Tung-Lam; Koffel, Thomas; Sanchez-Palencia, Laurent

    2013-12-01

    We study the competition between one-body and two-body couplings in weakly interacting two-component Bose gases, in particular as regards field correlations. We derive the mean-field theory for both ground-state and low-energy pair excitations in the general case where both one-body and two-body couplings are position dependent and the fluid is subjected to a state-dependent trapping potential. General formulas for phase and density correlations are also derived. Focusing on the case of homogeneous systems, we discuss the pair-excitation spectrum and the corresponding excitation modes, and use them to calculate correlation functions, including both quantum and thermal fluctuation terms. We show that the relative phase of the two components is imposed by that of the one-body coupling, while its fluctuations are determined by the modulus of the one-body coupling and by the two-body coupling. One-body coupling and repulsive two-body coupling cooperate to suppress relative-phase fluctuations, while attractive two-body coupling tends to enhance them. Further applications of the formalism presented here and extensions of our work are also discussed.

  19. Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction.

    PubMed

    Gu, Xiaodong; Huang, Ying; Levison, Bruce S; Gerstenecker, Gary; DiDonato, Anthony J; Hazen, Leah B; Lee, Joonsue; Gogonea, Valentin; DiDonato, Joseph A; Hazen, Stanley L

    2016-01-22

    Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815-3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to lipid surfaces poses considerable methodological challenges. Here we describe a new strategy that uses a novel synthetic photoactivatable and click chemistry-taggable phospholipid probe, which, when incorporated into HDL, was used to identify amino acid residues on PON1 that directly interact with the lipoprotein phospholipid surface. Several specific PON1 residues (Leu-9, Tyr-185, and Tyr-293) were identified through covalent cross-links with the lipid probes using affinity isolation coupled to liquid chromatography with on-line tandem mass spectrometry. Based upon the crystal structure for PON1, the identified residues are all localized in relatively close proximity on the surface of PON1, defining a domain that binds to the HDL lipid surface. Site-specific mutagenesis of the identified PON1 residues (Leu-9, Tyr-185, and Tyr-293), coupled with functional studies, reveals their importance in PON1 binding to HDL and both PON1 catalytic activity and stability. Specifically, the residues identified on PON1 provide important structural insights into the PON1-HDL interaction. More generally, the new photoactivatable and affinity-tagged lipid probe developed herein should prove to be a valuable tool for identifying contact sites supporting protein interactions with lipid interfaces such as found on cell membranes

  20. Two-body wear resistance of some indirect composite resins.

    PubMed

    Savabi, Omid; Nejatidanesh, Farahnaz; Shabanian, Mitra; Anbari, Zahra

    2011-06-01

    The aim of this study was to evaluate two-body wear of five indirect composites and compare them with enamel. Signum, belleGlass HP, SR Adoro, Dialog, GC Gradia and enamel were formed into cylinders (n = 10). Two-body abrasive wear rates were determined using a porcelain disk and a pin on disk apparatus. The height and weight loss of the specimens were measured by stereomicroscope and digital scale. The data were subjected to analysis of variance and Tukey HSD tests to determine significant differences (alpha = 0.05). GC Gradia showed significantly less wear resistance than the other materials. Enamel was more resistant than any of the tested composites. Within the limitations of this study it can be concluded that the type of resin, filler size and method of polymerization could have affect the two-body abrasion resistance of indirect composites. PMID:21780731

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

    PubMed

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

    2015-01-15

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

  2. Constraints on two-body lepton flavor violating decay processes

    SciTech Connect

    Nussinov, S.; Peccei, R. D.; Zhang, X. M.

    2001-01-01

    Simple ''unitarity inspired'' relations between two- and three-body lepton flavor violating decays are noted and discussed. In the absence of cancellations, the existing strong bounds on {mu}{yields}3e and {mu}{yields}e{gamma}{gamma} severely constrain two-body lepton flavor violating decays.

  3. Two-Body and Three-Body Atomic Recombination Reactions.

    ERIC Educational Resources Information Center

    Alvarino, Jose M.; Martinez, E.

    1983-01-01

    Discusses how, in some circumstances, a two-body reaction (association in absence of a third body) is the only possible association, and how reactions proceed in this case. Taking competition between two/three-body reactions into account, considers relative importance of such combinations and conditions under which the former can be competitive.…

  4. A transformation of the two-body problem

    NASA Technical Reports Server (NTRS)

    Bond, V. R.

    1985-01-01

    A transformation of the differential equations of motion of the two-body problem in the spherical coordinates to oscillator form is derived. It is shown that the independent variable transformation dt/ds = r squared is a transformation which makes the oscillator form possible.

  5. RANS Simulation of the Heave Response of a Two-Body Floating Point Wave Absorber: Preprint

    SciTech Connect

    Yu, Y.; Li, Y.

    2011-03-01

    A preliminary study on a two-body floating wave absorbers is presented in this paper. A Reynolds-Averaged Navier-Stokes computational method is applied for analyzing the hydrodynamic heave response of the absorber in operational wave conditions. The two-body floating wave absorber contains a float section and a submerged reaction section. For validation purposes, our model is first assumed to be locked. The two sections are forced to move together with each other. The locked single body model is used in a heave decay test, where the RANS result is validated with the experimental measurement. For the two-body floating point absorber simulation, the two sections are connected through a mass-spring-damper system, which is applied to simulate the power take-off mechanism under design wave conditions. Overall, the details of the flow around the absorber and its nonlinear interaction with waves are investigated, and the power absorption efficiency of the two-body floating wave absorber in waves with a constant value spring-damper system is examined.

  6. Contributions of conserved serine residues to the interactions of ligands with dopamine D2 receptors.

    PubMed

    Cox, B A; Henningsen, R A; Spanoyannis, A; Neve, R L; Neve, K A

    1992-08-01

    Four dopamine D2 receptor mutants were constructed, in each of which an alanine residue was substituted for one of four conserved serine residues, i.e., Ser-193, Ser-194, Ser-197, and Ser-391. Wild-type and mutant receptors were expressed transiently in COS-7 cells and stably in C6 glioma cells for analysis of ligand-receptor interactions. In radioligand binding assays, the affinity of D2 receptors for dopamine was decreased 50-fold by substitution of alanine for Ser-193, implicating this residue in the binding of dopamine. Each mutant had smaller decreases in affinity for one or more of the ligands tested, with no apparent relationship between the class of ligand and the pattern of mutation-induced changes in affinity, except that the potency of agonists was decreased by substitution for Ser-193. The potency of dopamine for inhibition of adenylyl cyclase was reduced substantially by substitution of alanine for Ser-193 or Ser-197. Mutation of Ser-194 led to a complete loss of efficacy for dopamine and p-tyramine, which would be consistent with an interaction between Ser-194 and the p-hydroxyl substituent of dopamine that is necessary for activation of the receptors to occur. Because mutation of the corresponding residues of beta 2-adrenergic receptors has very different consequences, we conclude that although the position of these serine residues is highly conserved among catecholamine receptors, and the residues as a group are important in ligand binding and activation of receptors by agonists, the function of each of the residues considered separately varies among catecholamine receptors. PMID:1321233

  7. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge-Charge Interactions.

    PubMed

    Tripathi, Swarnendu; Garcìa, Angel E; Makhatadze, George I

    2015-10-15

    Charge-charge interactions play an important role in thermal stability of proteins. We employed an all-atom, native-topology-based model with non-native electrostatics to explore the interplay between folding dynamics and stability of TNfn3 (the third fibronectin type III domain from tenascin-C). Our study elucidates the role of charge-charge interactions in modulating the folding energy landscape. In particular, we found that incorporation of explicit charge-charge interactions in the WT TNfn3 induces energetic frustration due to the presence of residual structure in the unfolded state. Moreover, optimization of the surface charge-charge interactions by altering the evolutionarily nonconserved residues not only increases the thermal stability (in agreement with previous experimental study) but also reduces the formation of residual structure and hence minimizes the energetic frustration along the folding route. We concluded that charge-charge interaction in the rationally designed TNfn3 plays an important role not only in enhancing the stability but also in assisting folding. PMID:26413861

  8. Atlas2bgeneral: Two-body resonance calculator

    NASA Astrophysics Data System (ADS)

    Gallardo, Tabaré

    2016-07-01

    For a massless test particle and given a planetary system, Atlas2bgeneral calculates all resonances in a given range of semimajor axes with all the planets taken one by one. Planets are assumed in fixed circular and coplanar orbits and the test particle with arbitrary orbit. A sample input data file to calculate the two-body resonances is available for use with the Fortran77 source code.

  9. Solitary solutions to a relativistic two-body problem

    NASA Astrophysics Data System (ADS)

    Marcinkevicius, R.; Navickas, Z.; Ragulskis, M.; Telksnys, T.

    2016-06-01

    Necessary and sufficient conditions for the existence of solitary solutions to a generalized model of a two-body problem perturbed by small post-Newtonian relativistic term are derived in this paper. It is demonstrated that kink, bright and dark solitary solutions exist in the model, when the relativistic effects are treated as higher order perturbations. Numerical experiments are used to verify theoretical results.

  10. Computational studies of protein-peptide interactions with systematic mutation of residues

    NASA Astrophysics Data System (ADS)

    Clare, Dominic F.; Clary, David C.

    2004-01-01

    The interactions between proteins and peptides in aqueous solution have been simulated using a molecular dynamics procedure with the systematic mutation of residues. An implicit solvent model has been used in post-processing to calculate the free energy of each of the complex, protein and peptide in solution and, subsequently, the binding free energy. Entropic contributions to the binding free energy have been estimated using classical ideal gas thermodynamics. A program has also been developed that systematically mutates each residue of the interacting peptide to alanine and determines the effect on the binding free energy. The interaction between the oncoprotein Mdm2 and the tumour suppressor peptide p53 has been used to test the method and reasonable agreement has been found with experiment and previous theoretical studies. The method has been extended to investigate the interaction between D10-p1, a mirror image D-peptide and potential Human Immunodeficiency Virus HIV-1 inhibitor, and IQN17, a model protein representing a potential drug target in the HIV-1 cell-cell fusion process. The key residues involved in the binding in each protein-peptide system have been identified and quantitative information on the significant factors in their importance have been obtained and compared with available experimental data.

  11. Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study.

    PubMed

    Keerthana, S P; Kolandaivel, P

    2015-04-01

    Cu-Zn superoxide dismutase 1 (SOD1) is a highly conserved bimetallic protein enzyme, used for the scavenging the superoxide radicals (O2 (-)) produced due to aerobic metabolism in the mitochondrial respiratory chain. Over 100 mutations have been identified and found to be in the homodimeric structure of SOD1. The enzyme has to be maintained in its dimeric state for the structural stability and enzymatic activity. From our investigation, we found that the mutations apart from the dimer interface residues are found to affect the dimer stability of protein and hence enhancing the aggregation and misfolding tendency of mutated protein. The homodimeric state of SOD1 is found to be held together by the non-covalent interactions. The molecular dynamics simulation has been used to study the hydrogen bond interactions between the dimer interface residues of the monomers in native and mutated forms of SOD1 in apo- and holo-states. The results obtained by this analysis reveal the fact that the loss of hydrogen bond interactions between the monomers of the dimer is responsible for the reduced stability of the apo- and holo-mutant forms of SOD1. The conformers with dimer interface residues in native and mutated protein obtained by the molecular dynamics simulation is subjected to quantum mechanical study using M052X/6-31G(d) level of theory. The charge transfer between N-H···O interactions in the dimer interface residues were studied. The weak interaction between the monomers of the dimer accounts for the reduced dimerization and enhanced deformation energy in the mutated SOD1 protein. PMID:25578810

  12. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    NASA Astrophysics Data System (ADS)

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-11-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants.

  13. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation.

    PubMed

    Aledo, Juan C; Cantón, Francisco R; Veredas, Francisco J

    2015-01-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

  14. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    PubMed Central

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-01-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

  15. A residue level protein-protein interaction model in electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Song, Xueyu

    2014-03-01

    The osmotic second virial coefficients B2 are directly related to the solubility of protein molecules in electrolyte solutions and can be useful to narrow down the search parameter space of protein crystallization conditions. Using a residue level model of protein-protein interaction in electrolyte solutions B2 of bovine pancreatic trypsin inhibitor and lysozyme in various solution conditions such as salt concentration, pH and temperature are calculated using an extended Fast Multipole Methods in combination with the boundary element formulation. Overall, the calculated B2 are well correlated with the experimental observations for various solution conditions. In combination with our previous work on the binding affinity calculations of protein complexes it is demonstrated that our residue level model can be used as a reliable model to describe protein-protein interaction in solutions.

  16. Infinity Manifold in Popovici's Photogravitational Two-Body Problem

    NASA Astrophysics Data System (ADS)

    Mioc, Vasile

    The two-body problem associated to the modified photogravitational law proposed by the Romanian astronomer Constantin Popovici is being resumed. After studying the equilibria and the collision manifold (Mioc and Blaga 2001) via the powerful tools of the qualitative analysis, here we tackle the escape/capture orbits. We start from the equations of motion established in the quoted paper, then we apply a mixed sequence of McGehee-type transformations of the first and second kind, obtaining new regular motion equations. In this way the infinity singularity is replaced by the infinity manifold, pasted on the phase space. The flow on this manifold is entirely described, pointing out special features.

  17. Heuristic judgment of mass ratio in two-body collisions.

    PubMed

    Gilden, D L; Proffitt, D R

    1994-12-01

    The logic of judging relative mass from a two-body collision is developed from data presented by Runeson and Vedeler (1993). Data from two experiments are analyzed on a point-by-point basis, and strong support for the theory that mass-ratio judgments are mediated by separate speed and angle heuristics is shown. This analysis is accomplished by reducing the collision event to two elementary features: the presence of ricochet and the ratio of exit speeds. The heuristics that both ricochet and greater exit speed specify relative lightness are shown to explain the basic patterns of data presented by Runeson and Vedeler. PMID:7816541

  18. Two-body problem of core-region coupled magnetic vortex stacks

    NASA Astrophysics Data System (ADS)

    Hänze, Max; Adolff, Christian F.; Velten, Sven; Weigand, Markus; Meier, Guido

    2016-02-01

    The dynamics of all four combinations of possible polarity and circularity states in a stack of two vortices is investigated by time-resolved scanning transmission x-ray microscopy. The vortex stacks are excited by unidirectional magnetic fields leading to a collective oscillation. Four different modes are observed that depend on the relative polarizations and circularities of the stacks. They are excited to a driven oscillation. We observe a repulsive and attractive interaction of the vortex cores depending on their relative polarizations. The nonlinearity of this core interaction results in different trajectories that describe a two-body problem.

  19. The RING 2.0 web server for high quality residue interaction networks.

    PubMed

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-01

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. PMID:27198219

  20. The RING 2.0 web server for high quality residue interaction networks

    PubMed Central

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C.E.

    2016-01-01

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico–chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain–domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π–π stacking and π–cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. PMID:27198219

  1. Conserved Residues of the Human Mitochondrial Holocytochrome c Synthase Mediate Interactions with Heme

    PubMed Central

    2015-01-01

    C-type cytochromes are distinguished by the covalent attachment of a heme cofactor, a modification that is typically required for its subsequent folding, stability, and function. Heme attachment takes place in the mitochondrial intermembrane space and, in most eukaryotes, is mediated by holocytochrome c synthase (HCCS). HCCS is the primary component of the eukaryotic cytochrome c biogenesis pathway, known as System III. The catalytic function of HCCS depends on its ability to coordinate interactions between its substrates: heme and cytochrome c. Recent advancements in the recombinant expression and purification of HCCS have facilitated comprehensive analyses of the roles of conserved residues in HCCS, as demonstrated in this study. Previously, we proposed a four-step model describing HCCS-mediated cytochrome c assembly, identifying a conserved histidine residue (His154) as an axial ligand to the heme iron. In this study, we performed a systematic mutational analysis of 17 conserved residues in HCCS, and we provide evidence that the enzyme contains two heme-binding domains. Our data indicate that heme contacts mediated by residues within these domains modulate the dynamics of heme binding and contribute to the stability of the HCCS–heme–cytochrome c steady state ternary complex. While some residues are essential for initial heme binding (step 1), others impact the subsequent release of the holocytochrome c product (step 4). Certain HCCS mutants that were defective in heme binding were corrected for function by exogenous aminolevulinic acid (ALA, the precursor to heme). This chemical “correction” supports the proposed role of heme binding for the corresponding residues. PMID:25054239

  2. Institutional Solutions to the ``Two-Body Problem"

    NASA Astrophysics Data System (ADS)

    Knezek, P.

    2005-05-01

    The Committee on the Status of Women (CSWA), in conjunction with the Employment Committee (EC), will hold a special session that will focus on institutional approaches to solving the ``two-body problem". In step with the national employment trend, for the majority of astronomers with partners, those partners work outside the home. This is particularly true for female astronomers, who generally are married to professionals (and often to other astronomers). Academic and professional institutions that employ the majority of astronomers are now beginning to recognize the importance of addressing what has come to be known as the ``two-body" problem in order to attract and retain the best scientists. A few of those institutions are making pioneering efforts to create pro-active approaches to the issue of dual-career couples. The special session will feature two or three speakers involved with the administration at institutions with pro-active policies. This special session will be coupled with the normal afternoon CSWA session, which will focus on the other side of the issue - how dual-career couples have successfully approached the issue at institutions that do NOT have proactive policies.

  3. Simple ``invariance'' of two-body decay kinematics

    NASA Astrophysics Data System (ADS)

    Agashe, Kaustubh; Franceschini, Roberto; Kim, Doojin

    2013-09-01

    We study the two-body decay of a mother particle into a massless daughter. We further assume that the mother particle is unpolarized and has a generic boost distribution in the laboratory frame. In this case, we show analytically that the laboratory frame energy distribution of the massless decay product has a peak, whose location is identical to the (fixed) energy of that particle in the rest frame of the corresponding mother particle. Given its simplicity and “invariance” under changes in the boost distribution of the mother particle, our finding should be useful for the determination of masses of mother particles. In particular, we anticipate that such a procedure will then not require a full reconstruction of this two-body decay chain (or, for that matter, information about the rest of the event). With this eventual goal in mind, we make a proposal for extracting the peak position by fitting the data to a well-motivated analytic function describing the shape of such an energy distribution. This fitting function is then tested on the theoretical prediction for top quark pair production and its decay, and it is found to be quite successful in this regard. As a proof of principle of the usefulness of our observation, we apply it for measuring the mass of the top quark at the LHC, using simulated data and including experimental effects.

  4. Empirical residual neutron-proton interaction in odd-odd nuclei

    NASA Astrophysics Data System (ADS)

    Wu, Zheying; Changizi, S. A.; Qi, Chong

    2016-03-01

    Two types of average neutron-proton interaction formulas are compared: In the first type, neutron-proton interactions for even-even and odd-A nuclei extracted from experimental binding energies show a smooth behavior as a function of mass number A and are dominated by the contribution from the symmetry energy. Whereas in the second type large systematic staggering is seen between even-A and odd-A nuclei. This deviation is understood in terms of the additional neutron-proton interaction in odd-odd nuclei relative to the neighboring even-even and odd-A systems. We explore three possible ways to extract this additional interaction from the binding energy difference of neighboring nuclei. The extracted interactions are positive in nearly all cases and show weak dependence on the mass number. The empirical interactions are also compared with theoretical values extracted from recent nuclear mass models where large unexpected fluctuations are seen in certain nuclei. The reproduction of the residual neutron-proton interaction and the correction of those irregular fluctuations can be a good criterion for the refinement of those mass models.

  5. Visualized kinematics code for two-body nuclear reactions

    NASA Astrophysics Data System (ADS)

    Lee, E. J.; Chae, K. Y.

    2016-05-01

    The one or few nucleon transfer reaction has been a great tool for investigating the single-particle properties of a nucleus. Both stable and exotic beams are utilized to study transfer reactions in normal and inverse kinematics, respectively. Because many energy levels of the heavy recoil from the two-body nuclear reaction can be populated by using a single beam energy, identifying each populated state, which is not often trivial owing to high level-density of the nucleus, is essential. For identification of the energy levels, a visualized kinematics code called VISKIN has been developed by utilizing the Java programming language. The development procedure, usage, and application of the VISKIN is reported.

  6. A detailed study of nonperturbative solutions of two-body Dirac equations

    SciTech Connect

    Crater, H.W.; Becker, R.L.; Wong, C.Y.; Van Alstine, P.

    1992-12-01

    In quark model calculations of the meson spectrums fully covariant two-body Dirac equations dictated by Dirac`s relativistic constraint mechanics gave a good fit to the entire meson mass spectrum for light quark mesons as well as heavy quark mesons with constituent world scalar and vector potentials depending on just one or two parameters. In this paper, we investigate the properties of these equations that made them work so well by solving them numerically for quantum electrodynamics (QED) and related field theories. The constraint formalism generates a relativistic quantum mechanics defined by two coupled Dirac equations on a sixteen component wave function which contain Lorentz covariant constituent potentials that are initially undetermined. An exact Pauli reduction leads to a second order relativistic Schroedinger-like equation for a reduced eight component wave function determined by an effective interaction -- the quasipotential. We first determine perturbatively to lowest order the relativistic quasipotential for the Schroedinger-like equation by comparing that form with one derived from the Bethe-Salpeter equation. Insertion of this perturbative information into the minimal interaction structures of the two-body Dirac equations then completely determines their interaction structures. Then we give a procedure for constructing the full sixteen component solution to our coupled first-order Dirac equations from a solution of the second order equation for the reduced wave function. Next, we show that a perturbative treatment of these equations yields the standard spectral results for QED and related interactions.

  7. A detailed study of nonperturbative solutions of two-body Dirac equations

    SciTech Connect

    Crater, H.W.; Becker, R.L.; Wong, C.Y.; Van Alstine, P.

    1992-12-01

    In quark model calculations of the meson spectrums fully covariant two-body Dirac equations dictated by Dirac's relativistic constraint mechanics gave a good fit to the entire meson mass spectrum for light quark mesons as well as heavy quark mesons with constituent world scalar and vector potentials depending on just one or two parameters. In this paper, we investigate the properties of these equations that made them work so well by solving them numerically for quantum electrodynamics (QED) and related field theories. The constraint formalism generates a relativistic quantum mechanics defined by two coupled Dirac equations on a sixteen component wave function which contain Lorentz covariant constituent potentials that are initially undetermined. An exact Pauli reduction leads to a second order relativistic Schroedinger-like equation for a reduced eight component wave function determined by an effective interaction -- the quasipotential. We first determine perturbatively to lowest order the relativistic quasipotential for the Schroedinger-like equation by comparing that form with one derived from the Bethe-Salpeter equation. Insertion of this perturbative information into the minimal interaction structures of the two-body Dirac equations then completely determines their interaction structures. Then we give a procedure for constructing the full sixteen component solution to our coupled first-order Dirac equations from a solution of the second order equation for the reduced wave function. Next, we show that a perturbative treatment of these equations yields the standard spectral results for QED and related interactions.

  8. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study.

    PubMed

    Bonet, Jaume; Caltabiano, Gianluigi; Khan, Abdul Kareem; Johnston, Michael A; Corbí, Carles; Gómez, Alex; Rovira, Xavier; Teyra, Joan; Villà-Freixa, Jordi

    2006-04-01

    Finding why protein-protein interactions (PPIs) are so specific can provide a valuable tool in a variety of fields. Statistical surveys of so-called transient complexes (like those relevant for signal transduction mechanisms) have shown a tendency of polar residues to participate in the interaction region. Following this scheme, residues in the unbound partners have to compete between interacting with water or interacting with other residues of the protein. On the other hand, several works have shown that the notion of active site electrostatic preorganization can be used to interpret the high efficiency in enzyme reactions. This preorganization can be related to the instability of the residues important for catalysis. In some enzymes, in addition, conformational changes upon binding to other proteins lead to an increase in the activity of the enzymatic partner. In this article the linear response approximation version of the semimacroscopic protein dipoles Langevin dipoles (PDLD/S-LRA) model is used to evaluate the stability of several residues in two phosphate hydrolysis enzymes upon complexation with their activating partners. In particular, the residues relevant for PPI and for phosphate hydrolysis in the CDK2/Cyclin A and Ras/GAP complexes are analyzed. We find that the evaluation of the stability of residues in these systems can be used to identify not only active site regions but it can also be used as a guide to locate "hot spots" for PPIs. We also show that conformational changes play a major role in positioning interfacing residues in a proper "energetic" orientation, ready to interact with the residues in the partner protein surface. Thus, we extend the preorganization theory to PPIs, extrapolating the results we obtained from the above-mentioned complexes to a more general case. We conclude that the correlation between stability of a residue in the surface and the likelihood that it participates in the interaction can be a general fact for transient

  9. Non multa, sed multum: Future lessons from two-prong, two-body decays of beauty

    SciTech Connect

    Bigi, I.I.; Stech, B.

    1987-12-01

    There are four two-body, two-prong decays modes of B mesons and two for beauty baryons and they are quite rare, i.e., their branching ratios are not expected to exceed the script O(10/sup -4/) level. Yet a detailed study of their relative rates with a sensitivity level of 10/sup -5/ can yield unique and important information on strong interactions. If the evolution of these reactions in proper time can be traced then, under favorable conditions, one can analyze B/sup 0/ - anti B/sup 0/ mixing and CP invariance in a detailed way. 4 refs.

  10. Structural Evolution in Atomic Nuclei: Residual Interactions, Quantum Phase Transitions and the Emergence of Collectivity

    SciTech Connect

    Casten, R. F.

    2007-10-26

    A synoptic view of the evolution of structure with Z and N in nuclei is beginning to emerge from the confiuence of new experimental results on phase transitional behavior, newly proposed many-body symmetries for critical point nuclei, a new generation of solvable collective models, powerful approaches to viewing the systematics of nuclear properties based on simple models of residual interactions, and advances in microscopic calculations of medium mass and heavy nuclei. A recent compilation of nuclear masses has contributed by permitting empirical extractions of new p-n interaction strengths of the last protons with the last neutrons in many nuclei across the nuclear chart. A number of these developments will be discussed with an eye to the opportunities and challenges they provide for the future, especially in the era of next-generation exotic beam facihties throughout the world.

  11. Material loss in two-body collisions during planet formation

    NASA Astrophysics Data System (ADS)

    Werner, J.; Schäfer, C.; Maindl, T. I.; Burger, C.; Speith, R.

    2016-02-01

    During the formation process of a terrestrial planet, a planetary embryo does not only accrete smaller dust particles but also suffers collisions with larger planetesimals. When simulating these collisions, most N-body codes treat them as perfect merging events, i.e. the resulting body's mass is the sum of the previous ones. In our work, we aim to determine whether this assumption is a justified simplification, specifically focusing on bodies containing volatile elements, such as water. To analyze this, we have developed a new Smooth Particle Hydrodynamics (SPH) code that includes elasto-plastic dynamics, a damage model for brittle materials and self gravity. It makes use of the Compute Unified Device Architecture (CUDA) and runs on modern GPU architectures which allows for higher resolution in less calculation time. This enables us to take a precise look at two-body collisions and determine the amount of both transferred and ejected mass according to specific parameters such as mass ratio of impactor and target, porosity, impact velocity, impact angle and water distribution.

  12. Orbit determination with the two-body integrals

    NASA Astrophysics Data System (ADS)

    Gronchi, G. F.; Dimare, L.; Milani, A.

    2010-07-01

    We investigate a method to compute a finite set of preliminary orbits for solar system bodies using the first integrals of the Kepler problem. This method is thought for the applications to the modern sets of astrometric observations, where often the information contained in the observations allows only to compute, by interpolation, two angular positions of the observed body and their time derivatives at a given epoch; we call this set of data attributable. Given two attributables of the same body at two different epochs we can use the energy and angular momentum integrals of the two-body problem to write a system of polynomial equations for the topocentric distance and the radial velocity at the two epochs. We define two different algorithms for the computation of the solutions, based on different ways to perform elimination of variables and obtain a univariate polynomial. Moreover we use the redundancy of the data to test the hypothesis that two attributables belong to the same body ( linkage problem). It is also possible to compute a covariance matrix, describing the uncertainty of the preliminary orbits which results from the observation error statistics. The performance of this method has been investigated by using a large set of simulated observations of the Pan-STARRS project.

  13. Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

    PubMed

    Ng, Derek P; Deber, Charles M

    2016-08-01

    Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes. PMID:27434090

  14. On the Mass Difference Between pi and rho Using a Relativistic Two-Body Model

    SciTech Connect

    Wong, Cheuk-Yin; Kim, Byeong-Noh; Crater, H. W.; Yoon, Jin-Hee

    2012-01-01

    The big mass difference between the pion(pi) and rho meson(rho) possibly originated from the spin-dependent nature of the interactions in the two states since these two states are similar except for spin. Both pi and rho are quark-antiquark systems which can be treated using the two-body Dirac equations (TBDE) of constraint dynamics. This relativistic approach for the two-body system has the advantage over the non-relativistic treatment in the sense that the spin-dependent nature is automatically coming out from the formalism. We employed Dirac's relativistic constraint dynamics to describe quark-antiquark systems. Within this formalism, the 16-component Dirac equation is reduced to the 4-component 2nd-order differential equation and the radial part of this equation is simply a Schroedinger-type equation with various terms calculated from the basic radial potential. We used a modified Richardson potential for quark-antiquark systems which satisfies the conditions of confinement and asymptotic freedom. We obtained the wave functions for these two mesons which are not singular at short distances. We also found that the cancellation between the Darwin and spin-spin interaction terms occurs in the pi mass but not in the rho mass, and this is the main source of the big difference in the two meson masses.

  15. One plus two-body random matrix ensembles with parity: Density of states and parity ratios

    SciTech Connect

    Vyas, Manan; Srivastava, P. C.; Kota, V. K. B.

    2011-06-15

    One plus two-body embedded Gaussian orthogonal ensemble of random matrices with parity [EGOE(1+2)-{pi}] generated by a random two-body interaction (modeled by GOE in two-particle spaces) in the presence of a mean field for spinless identical fermion systems is defined, generalizing the two-body ensemble with parity analyzed by Papenbrock and Weidenmueller [Phys. Rev. C 78, 054305 (2008)], in terms of two mixing parameters and a gap between the positive ({pi}=+) and negative ({pi}=-) parity single-particle (sp) states. Numerical calculations are used to demonstrate, using realistic values of the mixing parameters appropriate for some nuclei, that the EGOE(1+2)-{pi} ensemble generates Gaussian form (with corrections) for fixed parity eigenvalue densities (i.e., state densities). The random matrix model also generates many features in parity ratios of state densities that are similar to those predicted by a method based on the Fermi-gas model for nuclei. We have also obtained, by applying the formulation due to Chang et al. [Ann. Phys. (NY) 66, 137 (1971)], a simple formula for the spectral variances defined over fixed-(m{sub 1},m{sub 2}) spaces, where m{sub 1} is the number of fermions in the positive parity sp states and m{sub 2} is the number of fermions in the negative parity sp states. Similarly, using the binary correlation approximation, in the dilute limit, we have derived expressions for the lowest two-shape parameters. The smoothed densities generated by the sum of fixed-(m{sub 1},m{sub 2}) Gaussians with lowest two-shape corrections describe the numerical results in many situations. The model also generates preponderance of positive parity ground states for small values of the mixing parameters, and this is a feature seen in nuclear shell-model results.

  16. Possible chirality in the doubly-odd {sup 198}Tl nucleus: Residual interaction at play

    SciTech Connect

    Lawrie, E. A.; Lawrie, J. J.; Bark, R. A.; Mullins, S. M.; Murray, S. H. T.; Vymers, P. A.; Maliage, S. M.; Masiteng, P. L.; Ramashidzha, T. M.; Sharpey-Schafer, J. F.; Shirinda, O.; Vieu, Ch.; Schueck, C.; Lindsay, R.; Mabala, G. K.; Ragnarsson, I.

    2008-08-15

    A candidate for chiral bands was found in {sup 198}Tl for the first time in a mass region of oblate (or nonaxial with {gamma}{>=}30 deg.) deformed nuclei. Two bands show very similar quasiparticle alignments, moments of inertia, and B(M1)/B(E2) ratios. They have a relative excitation energy of about 500 keV and different patterns of energy staggering. Calculations using the two-quasiparticle-plus-triaxial-rotor model with residual proton-neutron interaction included show that a triaxial deformation with {gamma}{approx}44 deg. agrees very well with all the experimental observations. Furthermore, considerable energy staggering for both partner bands was calculated for this {pi}h{sub 9/2} x {nu}i{sub 13/2}{sup -1} configuration at {gamma}{approx}30 deg., suggesting that chiral bands may have substantial energy staggering.

  17. Ultralow field magnetization reversal of two-body Stoner particles system

    NASA Astrophysics Data System (ADS)

    Li, Fei; Lu, Xiaofeng; Tang, Rujun; Sun, Z. Z.

    Magnetic mechanism of nanoparticles has attracted explosive attention in the development of modern information industry. On the base of Landau-Lifshitz-Gilbert equation, we studied the magnetization reversal in a system of two Stoner particles with uniaxial anisotropies and static magnetic interaction. Using micromagnetic simulation, two typical geometrical configurations of perpendicular(PERP) and parallel(PARA) configuration where the diameter of each particle is 20nm are considered. We found that when the separation between two particles has 23nm in PERP configuration ultralow switching field strength, 17mT can be realized, which satisfies the zero-field condition in our previous works[J. Appl. Phys. 109, 104303(2011)] according to the chosen parameters of cobalt material. For other separation values the switching field are multiple of lowest field. However, in PARA configuration the switching field changes with the separation faintly. This two-body system considered in our work might be implement as a composite information bit and our results offer further possibilities for its applications in information storage and/or fast magnetic response. Ultralow field magnetization reversal of two-body Stoner particles system.

  18. A Failure to Communicate: MYOSIN RESIDUES INVOLVED IN HYPERTROPHIC CARDIOMYOPATHY AFFECT INTER-DOMAIN INTERACTION.

    PubMed

    Kronert, William A; Melkani, Girish C; Melkani, Anju; Bernstein, Sanford I

    2015-12-01

    Our molecular modeling studies suggest a charge-dependent interaction between residues Glu-497 in the relay domain and Arg-712 in the converter domain of human β-cardiac myosin. To test the significance of this putative interaction, we generated transgenic Drosophila expressing indirect flight muscle myosin with charge reversal mutations in the relay (E496R) or converter (R713E). Each mutation yielded dramatic reductions in myosin Ca-ATPase activity (~80%) as well as in basal (~67%) and actin-activated (~84%) Mg-ATPase activity. E496R myosin-induced in vitro actin-sliding velocity was reduced by 71% and R713E myosin permitted no actin motility. Indirect flight muscles of late pupae from each mutant displayed disrupted myofibril assembly, with adults having severely abnormal myofibrils and no flight ability. To understand the molecular basis of these defects, we constructed a putative compensatory mutant that expresses myosin with both E496R and R713E. Intriguingly, ATPase values were restored to ~73% of wild-type and actin-sliding velocity increased to 40%. The double mutation suppresses myofibril assembly defects in pupal indirect flight muscles and dramatically reduces myofibril disruption in young adults. Although sarcomere organization is not sustained in older flies and flight ability is not restored in homozygotes, young heterozygotes fly well. Our results indicate that this charge-dependent interaction between the myosin relay and converter domains is essential to the mechanochemical cycle and sarcomere assembly. Furthermore, the same inter-domain interaction is disrupted when modeling human β-cardiac myosin heavy chain cardiomyopathy mutations E497D or R712L, implying that abolishing this salt bridge is one cause of the human disease. PMID:26446785

  19. Is There a Preferential Interaction between Cholesterol and Tryptophan Residues in Membrane Proteins?†

    PubMed Central

    Holt, Andrea; de Almeida, Rodrigo F. M.; Nyholm, Thomas K. M.; Loura, Luís M. S.; Daily, Anna E.; Staffhorst, Rutger W. H. M.; Rijkers, Dirk T. S.; Koeppe, Roger E.; Prieto, Manuel; Killian, J. Antoinette

    2008-01-01

    Recently, several indications have been found that suggest a preferential interaction between cholesterol and tryptophan residues located near the membrane–water interface. The aim of this study was to investigate by direct methods how tryptophan and cholesterol interact with each other and what the possible consequences are for membrane organization. For this purpose, we used cholesterol-containing model membranes of dimyristoylphosphatidylcholine (DMPC) in which a transmembrane model peptide with flanking tryptophans [acetyl-GWW(LA)8LWWA-amide], called WALP23, was incorporated to mimic interfacial tryptophans of membrane proteins. These model systems were studied with two complementary methods. (1) Steady-state and time-resolved Förster resonance energy transfer (FRET) experiments employing the fluorescent cholesterol analogue dehydroergosterol (DHE) in combination with a competition experiment with cholesterol were used to obtain information about the distribution of cholesterol in the bilayer in the presence of WALP23. The results were consistent with a random distribution of cholesterol which indicates that cholesterol and interfacial tryptophans are not preferentially located next to each other in these bilayer systems. (2) Solid-state 2H NMR experiments employing either deuterated cholesterol or indole ring-deuterated WALP23 peptides were performed to study the orientation and dynamics of both molecules. The results showed that the quadrupolar splittings of labeled cholesterol were not affected by an interaction with tryptophan-flanked peptides and, vice versa, that the quadrupolar splittings of labeled indole rings in WALP23 are not significantly influenced by addition of cholesterol to the bilayer. Therefore, both NMR and fluorescence spectroscopy results independently show that, at least in the model systems studied here, there is no evidence for a preferential interaction between cholesterol and tryptophans located at the bilayer interface. PMID

  20. Accurate prediction of helix interactions and residue contacts in membrane proteins.

    PubMed

    Hönigschmid, Peter; Frishman, Dmitrij

    2016-04-01

    Accurate prediction of intra-molecular interactions from amino acid sequence is an important pre-requisite for obtaining high-quality protein models. Over the recent years, remarkable progress in this area has been achieved through the application of novel co-variation algorithms, which eliminate transitive evolutionary connections between residues. In this work we present a new contact prediction method for α-helical transmembrane proteins, MemConP, in which evolutionary couplings are combined with a machine learning approach. MemConP achieves a substantially improved accuracy (precision: 56.0%, recall: 17.5%, MCC: 0.288) compared to the use of either machine learning or co-evolution methods alone. The method also achieves 91.4% precision, 42.1% recall and a MCC of 0.490 in predicting helix-helix interactions based on predicted contacts. The approach was trained and rigorously benchmarked by cross-validation and independent testing on up-to-date non-redundant datasets of 90 and 30 experimental three dimensional structures, respectively. MemConP is a standalone tool that can be downloaded together with the associated training data from http://webclu.bio.wzw.tum.de/MemConP. PMID:26851352

  1. Polyunsaturated fatty acids inhibit Kv1.4 by interacting with positively charged extracellular pore residues.

    PubMed

    Farag, N E; Jeong, D; Claydon, T; Warwicker, J; Boyett, M R

    2016-08-01

    Polyunsaturated fatty acids (PUFAs) modulate voltage-gated K(+) channel inactivation by an unknown site and mechanism. The effects of ω-6 and ω-3 PUFAs were investigated on the heterologously expressed Kv1.4 channel. PUFAs inhibited wild-type Kv1.4 during repetitive pulsing as a result of slowing of recovery from inactivation. In a mutant Kv1.4 channel lacking N-type inactivation, PUFAs reversibly enhanced C-type inactivation (Kd, 15-43 μM). C-type inactivation was affected by extracellular H(+) and K(+) as well as PUFAs and there was an interaction among the three: the effect of PUFAs was reversed during acidosis and abolished on raising K(+) Replacement of two positively charged residues in the extracellular pore (H508 and K532) abolished the effects of the PUFAs (and extracellular H(+) and K(+)) on C-type inactivation but had no effect on the lipoelectric modulation of voltage sensor activation, suggesting two separable interaction sites/mechanisms of action of PUFAs. Charge calculations suggest that the acidic head group of the PUFAs raises the pKa of H508 and this reduces the K(+) occupancy of the selectivity filter, stabilizing the C-type inactivated state. PMID:27281482

  2. Study on fluorescence spectra of chlorothalonil residues and the interaction between chlorothalonil and Chinese herbal medicines.

    PubMed

    Ji, Ren-dong; Zhao, Zhi-min; Chen, Meng-lan; Wang, Le-xin; Zhu, Xing-yue

    2015-02-01

    The fluorescence spectrum was studied for the chlorothalonil (0.2928 mg x mL(-1)) using spectrofluorophotometer. The experiment results showed that the characteristic peaks (352 and 366 nm) are found in the spectrum of chlorothalonil standard solution when the excitation wavelength is 320 nm. And it was found that the shoulder peak gradually disappeared at 366 nm, while the fluorescence peak is stable at 352 nm with the decline of the solution concentration The exponential functional relationship between the concentration of chlorothalonil and fluorescence intensity at 352 nm was obtained, and its correlation coefficient is 0.999. The experimental results are consistent with the theoretical formula about fluorescence intensity and concentration The prediction model functions were also obtained through the liner fitting to the chlorothalonil solution of low concentration, and the correlation coefficient is 0. 995. The limit of detection (LOD) is 0.0188 microg x mL(-1), the limit of quantification (LOQ) is 0.0627 microg x mL(-1), and the linear range is 0.0627-28.45 microg x mL(-1). And fluorescence spectra were studied for the mixed system of astragalus, medlar and chlorothalonil. It was found that the fluorescence intensity of chlorothalonil solution is all declined with the addition of two kinds of Chinese Herbal Medicines, which indicates that there is an interaction between them. The decay rate of fluorescence intensity was obtained which is 88.5% and 99.7%, respectively. Then the model functions were established between fluorescence intensity and the volume of addition, and the correlation coefficient is 0.994 and 0.997, respectively. This study provides the experimental foundation for the detection of chlorothalonil residues using fluorescence spectrum. It is shown that it is possible to detect pesticide residues of chlorothalonil using fluorescence spectra directly, and the relevant parameter value satisfied the requirement of testing standard. Therefore

  3. Effect of Tensor Range in Nuclear Two-Body Problems

    DOE R&D Accomplishments Database

    Feshbach, H.; Schwinger, J.; Harr, J. A.

    1949-11-01

    The interaction between neutron and proton in the triplet state is investigated, a wide variation in the values of both central and tensor ranges are included; the per cent D state in the deuteron and the effective triplet range have been computed; the results are applied tot he discussion of the magnetic moment of the deuteron, the photoelectric disintegration of the deuteron, and neutron-proton scattering.

  4. Non-Collision Singularities in the Planar Two-Center-Two-Body Problem

    NASA Astrophysics Data System (ADS)

    Xue, Jinxin; Dolgopyat, Dmitry

    2016-06-01

    In this paper, we study a restricted four-body problem called the planar two-center-two-body problem. In the plane, we have two fixed centers Q 1 and Q 2 of masses 1, and two moving bodies Q 3 and Q 4 of masses {μ≪ 1} . They interact via Newtonian potential. Q 3 is captured by Q 2, and Q 4 travels back and forth between two centers. Based on a model of Gerver, we prove that there is a Cantor set of initial conditions that lead to solutions of the Hamiltonian system whose velocities are accelerated to infinity within finite time avoiding all earlier collisions. This problem is a simplified model for the planar four-body problem case of the Painlevé conjecture.

  5. Non-Collision Singularities in the Planar Two-Center-Two-Body Problem

    NASA Astrophysics Data System (ADS)

    Xue, Jinxin; Dolgopyat, Dmitry

    2016-08-01

    In this paper, we study a restricted four-body problem called the planar two-center-two-body problem. In the plane, we have two fixed centers Q 1 and Q 2 of masses 1, and two moving bodies Q 3 and Q 4 of masses {μ≪ 1}. They interact via Newtonian potential. Q 3 is captured by Q 2, and Q 4 travels back and forth between two centers. Based on a model of Gerver, we prove that there is a Cantor set of initial conditions that lead to solutions of the Hamiltonian system whose velocities are accelerated to infinity within finite time avoiding all earlier collisions. This problem is a simplified model for the planar four-body problem case of the Painlevé conjecture.

  6. The residual interaction of bound nucleons-two-nucleon matrix elements deduced from transfer experiments

    NASA Astrophysics Data System (ADS)

    Daehnick, W. W.

    1983-07-01

    Matrix elements for the effective two-nucleon interaction have been deduced from the population of multiplets near closed shells as observed in direct transfer reactions. In the evaluation, the limited purity of such multiples was taken into consideration, typically by weighting the observed fractions of the two-nucleon configurations by their spectroscopic strenghts and by using the resulting energy centroids. In a few cases, off-diagonal matrix elements are available from empirical wave funcitons. The systematic errors for particle-particle matrix elements extracted directly and those obtained from Pandya transformations were found to go in opposite directions. In some cases, this feautre of the empirical mehtod could be used to suggest upper and lower “bounds” for the extracted matrix elements. Diagonal matrix elements for the empirical residual interaction show a number of features suggestive of an underlying simplicity in the interaction of bound nucleons. Within experimental uncertainties (of about 10% for T=0 matrix elements) the monopole parts of the matrix elements are fit well with a simple A-0.75 dependence, and the data available to date do not reveal any significant monopole dependence on the quantum numbers of the interacting nucleons. The usefulness of scaling is suggested. Generally, diagonal matrix elements EJ( j1, j2) normalized by the extracted A-dependent monopole strength agree within expected experimental uncertainties whether derived from particle-particle or particle-hole multiples and whether extracted from the beginning or the end of a major shell. For values J≠0, the diagonal EJ( j2) matrix elements seem to follow two universal functions which depend on the semi-classical coupling angles θ 12, but are otherwise independent on j. For j1≠ j2 several “typical” functions ƒ(θ 12) can be constructed which fit subsets of the data and differ in a predictable way. The general features of the bound-nucleon interaction appear

  7. Interactions between allelochemicals and the microbial community affect weed suppresion following cover crop residue incorporation into soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study is to understand how soil microorganisms interact with cover crop-derived allelochemicals to suppress weed germination and growth following cover crop residue incorporation. We conducted a time series experiment by crossing sterilized and non-sterilized soil with four dif...

  8. Two-quasiparticle isomer, E1 hindrances and residual interactions in {sup 172}Tm

    SciTech Connect

    Hughes, R. O.; Lane, G. J.; Dracoulis, G. D.; Kibedi, T.; Nieminen, P.; Watanabe, H.

    2008-04-15

    The structure of the neutron-rich nucleus {sup 172}Tm has been studied using incomplete fusion of {sup 7}Li on an {sup 170}Er target at 30 MeV. A 190-{mu}s isomer at an excitation energy of 476 keV was identified using chopped beams and {gamma}-ray spectroscopy. The isomer decays with very inhibited E1 transitions to the rotational bands based on the parallel and antiparallel couplings of the {nu}5/2{sup -}[512] x {pi}1/2{sup +}[411] configuration, the latter (K{sup {pi}}=2{sup -}) being the ground state. The isomeric state has been assigned J{sup {pi}}=6{sup +}, arising from the energetically favored (parallel) coupling of the {nu}5/2{sup -}[512] x {pi}7/2{sup -}[523] configuration. The proton-neutron residual interaction was deduced for the configuration of the isomeric state and is found to agree with previous empirical studies.

  9. Residue Coulomb Interaction Among Isobars and Its Influence in Symmetry Energy of Neutron-Rich Fragment

    NASA Astrophysics Data System (ADS)

    Ma, Chun-Wang; Wang, Shan-Shan; Zhang, Yan-Li; Zhao, Yi-Long; Wei, Hui-Ling

    2015-09-01

    The residue Coulomb interaction (RCI), which affects the result of symmetry-energy coefficient of neutron-rich nucleus in isobaric yield ratio (IYR) method, is difficult to be determined. Four RCI approximations are investigated: (i) The M1-RCI adopting the ac/T (the ratio of Coulomb energy coefficient to temperature) determined from the IYR of mirror-nucleus fragments; (ii) The M2-RCI by fitting the difference between IYRs; (iii) The M3-RCI adopting the standard Coulomb energy at a temperature T = 2 MeV; and (iv) Neglecting the RCI among isobars. The M1-, M2- and M3-RCI are no larger than 0.4. In particular, the M2-RCI is very close to zero. The effects of RCI in asym/T of fragment are also studied. The M1- and M4-asym/T are found to be the lower and upper limitations of asym/T, respectively. The M2-asym/T overlaps the M4-asym/T, which indicates that the M2-RCI is negligible in the IYR method, and the RCI among the three isobars can be neglected. The relative consistent low values of M3-asym/T (7.5 ± 2.5) are found in very neutron-rich isobars. Supported by the Program for Science & Technology Innovation Talents in Universities of Henan Province (13HASTIT046), and Young Teacher Project in Henan Normal University (HNU), China

  10. On the question of current conservation for the two-body Dirac equations of constraint theory

    NASA Astrophysics Data System (ADS)

    Lienert, Matthias

    2015-08-01

    The two-body Dirac (2BD) equations of constraint theory are of special interest not only in view of applications for phenomenological calculations of mesonic spectra but also because they avoid no-go theorems about relativistic interactions. Furthermore, they provide a quantum mechanical description in a manifestly Lorentz invariant way using the concept of a multi-time wave function. In this paper, we place them into the context of the multi-time formalism of Dirac, Tomonaga and Schwinger for the first time. A general physical and mathematical framework is outlined and the mechanism which permits relativistic interaction is identified. The main requirement derived from the general framework is the existence of conserved tensor currents with a positive component which can play the role of a probability density. We analyze this question for a general class of 2BD equations thoroughly and comprehensively. While the free Dirac current is not conserved, it is possible to find replacements. Improving on previous research, we achieve definite conclusions whether restrictions of the function space or of the interaction terms can guarantee the positive definiteness of the currents—and whether such restrictions are physically adequate. The consequences of the results are drawn, with respect to both applied and foundational perspectives.

  11. Standardization of a Volumetric Displacement Measurement for Two-Body Abrasion Scratch Test Data Analysis

    NASA Technical Reports Server (NTRS)

    Street, K. W. Jr.; Kobrick, R. L.; Klaus, D. M.

    2011-01-01

    A limitation has been identified in the existing test standards used for making controlled, two-body abrasion scratch measurements based solely on the width of the resultant score on the surface of the material. A new, more robust method is proposed for analyzing a surface scratch that takes into account the full three-dimensional profile of the displaced material. To accomplish this, a set of four volume- displacement metrics was systematically defined by normalizing the overall surface profile to denote statistically the area of relevance, termed the Zone of Interaction. From this baseline, depth of the trough and height of the plowed material are factored into the overall deformation assessment. Proof-of-concept data were collected and analyzed to demonstrate the performance of this proposed methodology. This technique takes advantage of advanced imaging capabilities that allow resolution of the scratched surface to be quantified in greater detail than was previously achievable. When reviewing existing data analysis techniques for conducting two-body abrasive scratch tests, it was found that the ASTM International Standard G 171 specified a generic metric based only on visually determined scratch width as a way to compare abraded materials. A limitation to this method was identified in that the scratch width is based on optical surface measurements, manually defined by approximating the boundaries, but does not consider the three-dimensional volume of material that was displaced. With large, potentially irregular deformations occurring on softer materials, it becomes unclear where to systematically determine the scratch width. Specifically, surface scratches on different samples may look the same from a top view, resulting in an identical scratch width measurement, but may vary in actual penetration depth and/or plowing deformation. Therefore, two different scratch profiles would be measured as having identical abrasion properties, although they differ

  12. Interaction between soil mineralogy and the application of crop residues on aggregate stability and hydraulic conductivity of the soil

    NASA Astrophysics Data System (ADS)

    Lado, M.; Kiptoon, R.; Bar-Tal, A.; Wakindiki, I. I. C.; Ben-Hur, M.

    2012-04-01

    One of the main goals of modern agriculture is to achieve sustainability by maintaining crop productivity while avoiding soil degradation. Intensive cultivation could lead to a reduction in soil organic matter that could affect the structure stability and hydraulic conductivity of the soil. Moreover, crops extract nutrients from the soil that are taken away from the field when harvested, and as a consequence, the addition of fertilizers to the soil is necessary to maintain crop productivity. One way to deal with these problems is to incorporate crop residues into the soil after harvest. Crop residues are a source of organic matter that could improve soil physical properties, such as aggregate stability and soil hydraulic conductivity. However, this effect could vary according to other soil properties, such as clay content, clay mineralogy, and the presence of other cementing materials in the soil (mainly carbonates and aluminum and iron oxides). In the present work, the interaction between the addition of chickpea crop residues to the soil and clay mineralogy on aggregate stability and saturated hydraulic conductivity were studied. Chickpea plant residues were added at a rate of 0.5% (w/w) to smectitic, kaolinitic, illitic and non-phyllosilicate soils from different regions. The soils without (control) and with chickpea residues were incubated for 0, 3, 7 and 30 days, and the saturated hydraulic conductivity of the soils was measured in columns after each incubation time. The response of hydraulic conductivity to the addition of residues and incubation time was different in the soils with various mineralogies, although in general, the addition of chickpea residues increased the saturated hydraulic conductivity as compared with the control soils. This positive effect of crop residues on hydraulic conductivity was mainly a result of improved aggregate stability and resistance to slaking during wetting.

  13. Complete characterization of the ground-space structure of two-body frustration-free Hamiltonians for qubits

    SciTech Connect

    Ji Zhengfeng; Wei Zhaohui; Zeng Bei

    2011-10-15

    The problem of finding the ground state of a frustration-free Hamiltonian carrying only two-body interactions between qubits is known to be solvable in polynomial time. It is also shown recently that, for any such Hamiltonian, there is always a ground state that is a product of single- or two-qubit states. However, it remains unclear whether the whole ground space is of any succinct structure. Here, we give a complete characterization of the ground space of any two-body frustration-free Hamiltonian of qubits. Namely, it is a span of tree tensor network states of the same tree structure. This characterization allows us to show that the problem of determining the ground-state degeneracy is as hard as, but no harder than, its classical analog.

  14. Critical regions and residues for self-interaction of grapevine leafroll-associated virus 2 protein p24.

    PubMed

    Liu, Qing; Guo, Ran; Li, Mingjun; Feng, Ming; Wang, Xianyou; Wang, Qi; Cheng, Yuqin

    2016-07-15

    The 24-kDa protein (p24) encoded by grapevine leafroll-associated virus 2 (GLRaV-2) is an RNA-silencing suppressor. In this work, a yeast two-hybrid system (YTHS) and bimolecular fluorescence complementation analyses showed that GLRaV-2 p24 can interact with itself, and that this interaction occurs in the cytoplasm of Nicotiana benthamiana cells. To identify the functional region(s) and crucial amino acid residues required for p24 self-interaction, various truncated and substitution mutants were generated. YTHS assay showed that in both homologous pairing and pairing with the wild-type p24, the functional regions mapped to aa 10-180 or 1-170 which contain, respectively, all seven α-helices or the first six α-helices and the N-terminal end (aa 1-9) of the protein. When only the full-length p24 was an interaction partner, the functional region of aa 1-170 could be further mapped to aa 1-140 which contains four α-helices plus most of the fifth α-helix. Further analysis with substitution mutants demonstrated that hydrophobic residues I35/F38/V85/V89/W149 and V162/L169/L170, which may, respectively, mediate the inter-domain interaction of the same p24 monomer and the tail-to-tail association between two p24 counterparts, are crucial for homotypic p24-p24 interaction. In addition, substitution of two basic residues-R2 or R86-of p24, which may play important functional roles in RNA binding, did not seem to affect self-interaction of the mutants in yeast but had obvious effects in plant cells. Taken together, our results demonstrate the functional regions and crucial amino acids for p24 self-interaction. PMID:27084306

  15. Experimental Investigations on Fatigue Damage and Residual Properties of Interacting Notched Woven E-Glass/Epoxy Composite

    NASA Astrophysics Data System (ADS)

    Bhaskara Rao, Pathakokila; Rama Krishna, Avasarala; Ramji, Koona; Satya Devi, Ambadipudi

    2015-10-01

    The interacting notched laminates of plain weave E-glass fiber reinforced with epoxy were fatigued at predetermined frequency in tension-tension to investigate the fatigue damage and residual properties. The results from stress-life curves summarize that damage growing around the notches due to stress concentration is the underlying cause for the variation in fatigue strengths among the geometrically different specimens considered. The residual strength and modulus decay with respect to cycle number at 50 % of the ultimate tensile strength were investigated. It is evident from the experimental data that the residual strength decreases with cycle number and increases due to redistribution of stress around the notches. The detailed study of the damage development under cyclic loads also explains the causes of modulus reduction for all the laminate geometries.

  16. Standardization of a Volumetric Displacement Measurement for Two-Body Abrasion Scratch Test Data Analysis

    NASA Technical Reports Server (NTRS)

    Kobrick, Ryan L.; Klaus, David M.; Street, Kenneth W., Jr.

    2010-01-01

    A limitation has been identified in the existing test standards used for making controlled, two-body abrasion scratch measurements based solely on the width of the resultant score on the surface of the material. A new, more robust method is proposed for analyzing a surface scratch that takes into account the full three-dimensional profile of the displaced material. To accomplish this, a set of four volume displacement metrics are systematically defined by normalizing the overall surface profile to statistically denote the area of relevance, termed the Zone of Interaction (ZOI). From this baseline, depth of the trough and height of the ploughed material are factored into the overall deformation assessment. Proof of concept data were collected and analyzed to demonstrate the performance of this proposed methodology. This technique takes advantage of advanced imaging capabilities that now allow resolution of the scratched surface to be quantified in greater detail than was previously achievable. A quantified understanding of fundamental particle-material interaction is critical to anticipating how well components can withstand prolonged use in highly abrasive environments, specifically for our intended applications on the surface of the Moon and other planets or asteroids, as well as in similarly demanding, harsh terrestrial settings

  17. Three-body scattering hypervolume for ultracold atoms with a model two-body potential

    NASA Astrophysics Data System (ADS)

    Zhu, Shangguo; Tan, Shina

    2015-05-01

    It has been known that the three-boson low energy effective interaction influences the dynamic and the static properties of many bosons, including the ground state energies of dilute Bose-Einstein condensates. The three-body scattering hypervolume, which is a three-body analogue of the two-body scattering length, characterizes this effective interaction. Surprisingly, knowledge of this fundamental quantity has still been lacking, except for hard sphere bosons and bosons with large scattering length. For bosons with a soft-ball potential--the repulsive Gaussian potential, we determine the scattering hypervolume by solving the three-body Schrödinger equation numerically, and matching the solution with the asymptotic expansions for the wave function at large hyperradii. Our analyses of the three-body scattering hypervolume can be extended to the long-range Van der Waals potential. They will be necessary in the precise understanding of the energetics and dynamics of three, more, or many ultracold bosonic atoms.

  18. The Role of Putative Phosphatidylserine-Interactive Residues of Tissue Factor on Its Coagulant Activity at the Cell Surface.

    PubMed

    Ansari, Shabbir A; Pendurthi, Usha R; Sen, Prosenjit; Rao, L Vijaya Mohan

    2016-01-01

    Exposure of phosphatidylserine (PS) on the outer leaflet of the cell membrane is thought to play a critical role in tissue factor (TF) decryption. Recent molecular dynamics simulation studies suggested that the TF ectodomain may directly interact with PS. To investigate the potential role of TF direct interaction with the cell surface phospholipids on basal TF activity and the enhanced TF activity following the decryption, one or all of the putative PS-interactive residues in the TF ectodomain were mutated and tested for their coagulant activity in cell systems. Out of the 9 selected TF mutants, five of them -TFS160A, TFS161A, TFS162A, TFK165A, and TFD180A- exhibited a similar TF coagulant activity to that of the wild-type TF. The specific activity of three mutants, TFK159A, TFS163A, and TFK166A, was reduced substantially. Mutation of the glycine residue at the position 164 markedly abrogated the TF coagulant activity, resulting in ~90% inhibition. Mutation of all nine lipid binding residues together did not further decrease the activity of TF compared to TFG164A. A similar fold increase in TF activity was observed in wild-type TF and all TF mutants following the treatment of THP-1 cells with either calcium ionomycin or HgCl2, two agents that are commonly used to decrypt TF. Overall, our data show that a few select TF residues that are implicated in interacting with PS contribute to the TF coagulant activity at the cell surface. However, our data also indicate that TF regions outside of the putative lipid binding region may also contribute to PS-dependent decryption of TF. PMID:27348126

  19. The Role of Putative Phosphatidylserine-Interactive Residues of Tissue Factor on Its Coagulant Activity at the Cell Surface

    PubMed Central

    Ansari, Shabbir A.; Pendurthi, Usha R.; Sen, Prosenjit; Rao, L. Vijaya Mohan

    2016-01-01

    Exposure of phosphatidylserine (PS) on the outer leaflet of the cell membrane is thought to play a critical role in tissue factor (TF) decryption. Recent molecular dynamics simulation studies suggested that the TF ectodomain may directly interact with PS. To investigate the potential role of TF direct interaction with the cell surface phospholipids on basal TF activity and the enhanced TF activity following the decryption, one or all of the putative PS-interactive residues in the TF ectodomain were mutated and tested for their coagulant activity in cell systems. Out of the 9 selected TF mutants, five of them -TFS160A, TFS161A, TFS162A, TFK165A, and TFD180A- exhibited a similar TF coagulant activity to that of the wild-type TF. The specific activity of three mutants, TFK159A, TFS163A, and TFK166A, was reduced substantially. Mutation of the glycine residue at the position 164 markedly abrogated the TF coagulant activity, resulting in ~90% inhibition. Mutation of all nine lipid binding residues together did not further decrease the activity of TF compared to TFG164A. A similar fold increase in TF activity was observed in wild-type TF and all TF mutants following the treatment of THP-1 cells with either calcium ionomycin or HgCl2, two agents that are commonly used to decrypt TF. Overall, our data show that a few select TF residues that are implicated in interacting with PS contribute to the TF coagulant activity at the cell surface. However, our data also indicate that TF regions outside of the putative lipid binding region may also contribute to PS-dependent decryption of TF. PMID:27348126

  20. Identification of an 11-residue portion of CTP-phosphocholine cytidylyltransferase that is required for enzyme-membrane interactions.

    PubMed Central

    Yang, J; Wang, J; Tseu, I; Kuliszewski, M; Lee, W; Post, M

    1997-01-01

    CTP-phosphocholine cytidylyltransferase (CT) is a key regulatory enzyme in the biosynthesis of phosphatidylcholine (PC) in many cells. Enzyme-membrane interactions appear to play an important role in CT activation. A putative membrane-binding domain appears to be located between residues 236 and 293 from the N-terminus. To map the membrane-binding domain more precisely, glutathione S-transferase fusion proteins were prepared that contained deletions of various domains in this putative lipid-binding region. The fusion proteins were assessed for their binding of [3H]PC/oleic acid vesicles. Fusion proteins encompassing residues 267-277 bound to PC/oleic acid vesicles, whereas fragments lacking this region exhibited no specific binding to the lipid vesicles. The membrane-binding characteristics of the CT fusion proteins were also examined using intact lung microsomes. Only fragments encompassing residues 267-277 competed with full-length 125I-labelled CT, expressed in recombinant Sf9 insect cells, for microsomal membrane binding. To investigate the role of this region in PC biosynthesis, A549 and L2 cells were transfected with cDNA for CT mutants under the control of a glucocorticoid-inducible long terminal repeat (LTR) promoter. Induction of CT mutants containing residues 267-277 in transfectants resulted in reduced PC synthesis. The decrease in PC synthesis was accompanied by a shift in endogenous CT activity from the particulate to the soluble fraction. Expression of CT mutants lacking this region in A549 and L2 cells did not affect PC formation and subcellular distribution of CT activity. These results suggest that the CT region located between residues 267 and 277 from the N-terminus is required for the interaction of CT with membranes. PMID:9224626

  1. Residual meson-meson interaction from lattice gauge simulation in a simple QED{sub 2+1} model

    SciTech Connect

    J. Canosa; H. Fiebig

    1995-08-01

    The residual interaction for a meson-meson system is computed utilizing the cumulant, or cluster, expansion of the momentum-space time correlation matrix. The cumulant expansion serves to define asymptotic, or free, meson-meson operators. The definition of an effective interaction is then based on a comparison of the full (interacting) and the free (noninteracting) time correlation matrices. The proposed method, which may straight forwardly be transcribed to other hadron-hadron systems, here is applied to a simple 2+1 dimensional U(1) lattice gauge model tuned such that it is confining. Fermions are treated in the staggered scheme. The effective interaction exhibits a repulsive core and attraction at intermediate relative distances. These findings are consistent with an earlier study of the same model utilizing L{umlt u}scher's method where scattering phase shifts are obtained directly.

  2. Lorentz Boosted Potential for a Two-Body System with Unequal Masses

    NASA Astrophysics Data System (ADS)

    Kamada, H.; Polyzou, W. N.; Witała, H.; Miyagawa, K.

    2014-04-01

    We produce a Lorentz boosted two-body potential for particles of different mass that is phase equivalent to a given realistic non-relativistic two-body potential. The relativistic potential is related to the nonrelativistic potential using the Coester-Pieper-Serduke scheme, which ensures that the same scattering wave functions are obtained from the relativistic and non-relativistic potentials. This implies that the phase shifts are identical functions of the relative momentum. To construct the potential we use an iterative scheme that generalizes one that has been applied successfully to two-body systems with equal masses.

  3. Two-Body Electrodisintegration of $^3$He at High Momentum Transfer

    SciTech Connect

    R. Schiavilla; O. Benhar; A. Kievsky; L.E. Marcucci; M. Viviani

    2005-08-01

    The {sup 3}He (e,e{prime}p)d reaction is studied using an accurate three-nucleon bound state wave function, a model for the electromagnetic current operator including one- and two-body terms, and the Glauber approximation for the treatment of final state interactions. In contrast to earlier studies, the profile operator in the Glauber expansion is derived from a nucleon-nucleon scattering amplitude, which retains its full spin and isospin dependence and is consistent with phase-shift analyses of two-nucleon scattering data. The amplitude is boosted from the center-of-mass frame, where parameterizations for it are available, to the frame where rescattering occurs. Exact Monte Carlo methods are used to evaluate the relevant matrix elements of the electromagnetic current operator. The predicted cross section is found to be in quantitative agreement with the experimental data for values of the missing momentum p{sub m} in the range (0--700) MeV/c, but underestimates the data at p{sub m} {approx} 1 GeV/c by about a factor of two. However, the longitudinal-transverse asymmetry, measured up to p{sub m} {approx} 600 MeV/c, is well reproduced by theory. A critical comparison is carried out between the results obtained in the present work and those of earlier studies.

  4. HIGH TEMPERATURE INTERACTIONS BETWEEN RESIDUAL OIL ASH AND DISPERSED KAOLINITE POWDERS

    EPA Science Inventory

    The potential use of sorbents to manage ultrafine ash aerosol emissions from residual oil combustion was investigated using a downfired 82-kW-rated laboratory-scale refractory-lined combustor. The major constituents were vanadium (V), iron (Fe), nickel, (Ni) and zinc (Zn). Of the...

  5. Role of acidic residues in helices TH8-TH9 in membrane interactions of the diphtheria toxin T domain.

    PubMed

    Ghatak, Chiranjib; Rodnin, Mykola V; Vargas-Uribe, Mauricio; McCluskey, Andrew J; Flores-Canales, Jose C; Kurnikova, Maria; Ladokhin, Alexey S

    2015-04-01

    The pH-triggered membrane insertion of the diphtheria toxin translocation domain (T domain) results in transferring the catalytic domain into the cytosol, which is relevant to potential biomedical applications as a cargo-delivery system. Protonation of residues is suggested to play a key role in the process, and residues E349, D352 and E362 are of particular interest because of their location within the membrane insertion unit TH8-TH9. We have used various spectroscopic, computational and functional assays to characterize the properties of the T domain carrying the double mutation E349Q/D352N or the single mutation E362Q. Vesicle leakage measurements indicate that both mutants interact with the membrane under less acidic conditions than the wild-type. Thermal unfolding and fluorescence measurements, complemented with molecular dynamics simulations, suggest that the mutant E362Q is more susceptible to acid destabilization because of disruption of native intramolecular contacts. Fluorescence experiments show that removal of the charge in E362Q, and not in E349Q/D352N, is important for insertion of TH8-TH9. Both mutants adopt a final functional state upon further acidification. We conclude that these acidic residues are involved in the pH-dependent action of the T domain, and their replacements can be used for fine tuning the pH range of membrane interactions. PMID:25875295

  6. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    PubMed

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. PMID:26867971

  7. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues

    PubMed Central

    Ando, Hideaki; Hirose, Matsumi; Gainche, Laura; Kawaai, Katsuhiro; Bonneau, Benjamin; Ijuin, Takeshi; Itoh, Toshiki; Takenawa, Tadaomi; Mikoshiba, Katsuhiko

    2015-01-01

    Phosphatidylinositol phosphate kinases (PIPKs) are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate) is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα) and type IIα (PIPKIIα) in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3− cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5)P2. PMID:26509711

  8. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    PubMed Central

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  9. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

    PubMed

    Tse, Amanda; Verkhivker, Gennady M

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  10. Spin-dependent two-body interactions from gravitational self-force computations

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Damour, Thibault; Geralico, Andrea

    2015-12-01

    We analytically compute, through the eight-and-a-half post-Newtonian order and the fourth-order in spin, the gravitational self-force correction to Detweiler's gauge invariant redshift function for a small mass in circular orbit around a Kerr black hole. Using the first law of mechanics for black hole binaries with spin [L. Blanchet, A. Buonanno and A. Le Tiec, Phys. Rev. D 87, 024030 (2013)] we transcribe our results into a knowledge of various spin-dependent couplings, as encoded within the spinning effective-one-body model of T. Damour and A. Nagar [Phys. Rev. D 90, 044018 (2014)]. We also compare our analytical results to the (corrected) numerical self-force results of A. G. Shah, J. L. Friedman and T. S. Keidl [Phys. Rev. D 86, 084059 (2012)], from which we show how to directly extract physically relevant spin-dependent couplings.

  11. Few Residues within an Extensive Binding Interface Drive Receptor Interaction and Determine the Specificity of Arrestin Proteins*

    PubMed Central

    Vishnivetskiy, Sergey A.; Gimenez, Luis E.; Francis, Derek J.; Hanson, Susan M.; Hubbell, Wayne L.; Klug, Candice S.; Gurevich, Vsevolod V.

    2011-01-01

    Arrestins bind active phosphorylated forms of G protein-coupled receptors, terminating G protein activation, orchestrating receptor trafficking, and redirecting signaling to alternative pathways. Visual arrestin-1 preferentially binds rhodopsin, whereas the two non-visual arrestins interact with hundreds of G protein-coupled receptor subtypes. Here we show that an extensive surface on the concave side of both arrestin-2 domains is involved in receptor binding. We also identified a small number of residues on the receptor binding surface of the N- and C-domains that largely determine the receptor specificity of arrestins. We show that alanine substitution of these residues blocks the binding of arrestin-1 to rhodopsin in vitro and of arrestin-2 and -3 to β2-adrenergic, M2 muscarinic cholinergic, and D2 dopamine receptors in intact cells, suggesting that these elements critically contribute to the energy of the interaction. Thus, in contrast to arrestin-1, where direct phosphate binding is crucial, the interaction of non-visual arrestins with their cognate receptors depends to a lesser extent on phosphate binding and more on the binding to non-phosphorylated receptor elements. PMID:21471193

  12. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

    PubMed

    Lipska, Agnieszka G; Seidman, Steven R; Sieradzan, Adam K; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A

    2016-05-14

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models. PMID:27179474

  13. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    NASA Astrophysics Data System (ADS)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  14. Validation of Proposed Metrics for Two-Body Abrasion Scratch Test Analysis Standards

    NASA Technical Reports Server (NTRS)

    Kobrick, Ryan L.; Klaus, David M.; Street, Kenneth W., Jr.

    2011-01-01

    The objective of this work was to evaluate a set of standardized metrics proposed for characterizing a surface that has been scratched from a two-body abrasion test. This is achieved by defining a new abrasion region termed Zone of Interaction (ZOI). The ZOI describes the full surface profile of all peaks and valleys, rather than just measuring a scratch width as currently defined by the ASTM G 171 Standard. The ZOI has been found to be at least twice the size of a standard width measurement, in some cases considerably greater, indicating that at least half of the disturbed surface area would be neglected without this insight. The ZOI is used to calculate a more robust data set of volume measurements that can be used to computationally reconstruct a resultant profile for detailed analysis. Documenting additional changes to various surface roughness parameters also allows key material attributes of importance to ultimate design applications to be quantified, such as depth of penetration and final abraded surface roughness. Data are presented to show that different combinations of scratch tips and abraded materials can actually yield the same scratch width, but result in different volume displacement or removal measurements and therefore, the ZOI method is more discriminating than the ASTM method scratch width. Furthermore, by investigating the use of custom scratch tips for our specific needs, the usefulness of having an abrasion metric that can measure the displaced volume in this standardized manner, and not just by scratch width alone, is reinforced. This benefit is made apparent when a tip creates an intricate contour having multiple peaks and valleys within a single scratch. This work lays the foundation for updating scratch measurement standards to improve modeling and characterization of three-body abrasion test results.

  15. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    NASA Astrophysics Data System (ADS)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  16. MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein–ligand fragment interaction, pathways and SNPs

    PubMed Central

    Tanramluk, Duangrudee; Narupiyakul, Lalita; Akavipat, Ruj; Gong, Sungsam; Charoensawan, Varodom

    2016-01-01

    Protein–ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein–ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein–ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein–ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org). PMID:27131358

  17. MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs.

    PubMed

    Tanramluk, Duangrudee; Narupiyakul, Lalita; Akavipat, Ruj; Gong, Sungsam; Charoensawan, Varodom

    2016-07-01

    Protein-ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein-ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein-ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein-ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org). PMID:27131358

  18. Role of portal region lysine residues in electrostatic interactions between heart fatty acid binding protein and phospholipid membranes.

    PubMed

    Herr, F M; Aronson, J; Storch, J

    1996-01-30

    The structure of heart fatty acid binding protein (HFABP) is a flattened beta-barrel comprising 10 antiparallel beta-sheets capped by two alpha-helical segments. The helical cap region is hypothesized to behave as a portal "lid" for the entry and release of ligand from the binding pocket. The transfer of fatty acid from HFABP is thought to occur via effective collisional interactions with membranes, and these interactions are enhanced when transfer is to membranes of net negative charge, thus implying that specific basic residues on the surface of HFABP may govern the transfer process [Wootan, M. G., & Storch, J. (1994) J. Biol. Chem. 269, 10517-10523]. To directly examine the role of charged lysine residues on the HFABP surface in specific interactions with membranes, chemical modification and selective mutagenesis of HFABP were used. All surface lysine residues were neutralized by acetylation of recombinant HFABP with acetic anhydride. In addition, seven mutant HFABPs were generated that resulted in charge alterations in five distinct sites of HFABP. Modification of the protein did not significantly alter the structural or ligand binding properties of HFABP, as assessed by circular dichroism, fluorescence quantum yield, and ligand binding analyses. By using a resonance energy transfer assay, transfer of 2-(9-anthroyloxy)palmitate (2AP) from acetylated HFABP to membranes was significantly slower than transfer from native HFABP. In addition, in distinct contrast to transfer from native protein, the 2AP transfer rate from acetylated HFABP was not increased to acceptor membranes of increased negative charge. Transfer of 2AP from HFABP mutants involving K22, located on alpha-helix I (alpha-I) of the helical cap region, was 3-fold slower than transfer from wild-type protein, whereas rates from a mutant involving the K59 residue, located on the beta 2-turn of the barrel near the helical cap, were 2-fold faster than those of wild type. A double mutant involving K22 and K

  19. Neutral weak-current two-body contributions in inclusive scattering from {sup 12}C

    SciTech Connect

    Lovato, Alessandro; Gandolfi, Stefano; Carlson, Joseph; Pieper, S. C.; Schiavilla, Rocco

    2014-05-01

    An {\\it ab initio} calculation of the sum rules of the neutral weak response functions in $^{12}$C is reported, based on a realistic Hamiltonian, including two- and three-nucleon potentials, and on realistic currents, consisting of one- and two-body terms. We find that the sum rules of the response functions associated with the longitudinal and transverse components of the (space-like) neutral current are largest and that a significant portion ($\\simeq 30$\\%) of the calculated strength is due to two-body terms. This fact may have implications for the MiniBooNE and other neutrino quasi-elastic scattering data on nuclei.

  20. Amino Acid Residues of RegA Important for Interactions with the CbbR-DNA Complex of Rhodobacter sphaeroides

    PubMed Central

    Dangel, Andrew W.; Luther, Amanda

    2014-01-01

    CbbR and RegA (PrrA) are transcriptional regulators of the Calvin-Benson-Bassham (CBB) CO2 fixation pathway (cbbI and cbbII) operons of Rhodobacter sphaeroides. The CbbR and RegA proteins interact, but CbbR must be bound to the promoter DNA in order for RegA-CbbR protein-protein interactions to occur. RegA greatly enhances the ability of CbbR to bind the cbbI promoter or greatly enhances the stability of the CbbR/promoter complex. The N-terminal receiver domain and the DNA binding domain of RegA were shown to interact with CbbR. Residues in α-helix 7 and α-helix 8 of the DNA binding domain (helix-turn-helix) of RegA directly interacted with CbbR, with α-helix 7 positioned immediately above the DNA and α-helix 8 located in the major groove of the DNA. A CbbR protein containing only the DNA binding motif and the linker helix was capable of binding to RegA. In contrast, a truncated CbbR containing only the linker helix and recognition domains I and II (required for effector binding) was not able to interact with RegA. The accumulated results strongly suggest that the DNA binding domains of both proteins interact to facilitate optimal transcriptional control over the cbb operons. In vivo analysis, using constitutively active mutant CbbR proteins, further indicated that CbbR must interact with phosphorylated RegA in order to accomplish transcriptional activation. PMID:24957624

  1. Effect of residual attractive interactions in size asymmetric colloidal mixtures: Theoretical analysis and predictions.

    PubMed

    Germain, Ph

    2010-07-28

    We analyze the influence of residual attractions on the static and some dynamic properties of size asymmetric mixtures of "hard-sphere-like" colloids. These attractions, usually neglected in the theoretical analysis, are characterized by a very short range and a moderate strength reflecting the underlying microscopic structure of the colloidal particles. Their effect on the potentials of mean force is analyzed from analytical expressions obtained from low density expansions. The effective potential of the big particle fluid is next considered. An analytical expression is proposed for estimating the deviation with respect to the hard sphere depletion potential. This case is compared to that of mixtures with noninteracting depletants. The important consequences on the binodals and the glass transition lines of the effective fluid are discussed in both cases. This study is next extended to other properties-the specific heat and the low shear viscosity-which incorporate contributions from the two components of the binary mixture. PMID:20687684

  2. Effect of residual attractive interactions in size asymmetric colloidal mixtures: Theoretical analysis and predictions

    NASA Astrophysics Data System (ADS)

    Germain, Ph.

    2010-07-01

    We analyze the influence of residual attractions on the static and some dynamic properties of size asymmetric mixtures of "hard-sphere-like" colloids. These attractions, usually neglected in the theoretical analysis, are characterized by a very short range and a moderate strength reflecting the underlying microscopic structure of the colloidal particles. Their effect on the potentials of mean force is analyzed from analytical expressions obtained from low density expansions. The effective potential of the big particle fluid is next considered. An analytical expression is proposed for estimating the deviation with respect to the hard sphere depletion potential. This case is compared to that of mixtures with noninteracting depletants. The important consequences on the binodals and the glass transition lines of the effective fluid are discussed in both cases. This study is next extended to other properties—the specific heat and the low shear viscosity—which incorporate contributions from the two components of the binary mixture.

  3. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

    PubMed Central

    Yip, Kevin Y; Kim, Philip M; McDermott, Drew; Gerstein, Mark

    2009-01-01

    Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. Results To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1) Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2) Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3) Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up opportunities for further

  4. MOWGLI: prediction of protein-MannOse interacting residues With ensemble classifiers usinG evoLutionary Information.

    PubMed

    Pai, Priyadarshini P; Mondal, Sukanta

    2016-10-01

    Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues to decipher the underlying mechanisms of protein-mannose interactions during infections. This study proposes an approach using an ensemble of base classifiers for prediction of MIR using their evolutionary information in the form of position-specific scoring matrix. The base classifiers are random forests trained by different subsets of training data set Dset128 using 10-fold cross-validation. The optimized ensemble of base classifiers, MOWGLI, is then used to predict MIR on protein chains of the test data set Dtestset29 which showed a promising performance with 92.0% accurate prediction. An overall improvement of 26.6% in precision was observed upon comparison with the state-of-art. It is hoped that this approach, yielding enhanced predictions, could be eventually used for applications in drug design and vaccine development. PMID:26457920

  5. NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

    PubMed Central

    2014-01-01

    Background The rapid growth of un-annotated missense variants poses challenges requiring novel strategies for their interpretation. From the thermodynamic point of view, amino acid changes can lead to a change in the internal energy of a protein and induce structural rearrangements. This is of great relevance for the study of diseases and protein design, justifying the development of prediction methods for variant-induced stability changes. Results Here we propose NeEMO, a tool for the evaluation of stability changes using an effective representation of proteins based on residue interaction networks (RINs). RINs are used to extract useful features describing interactions of the mutant amino acid with its structural environment. Benchmarking shows NeEMO to be very effective, allowing reliable predictions in different parts of the protein such as β-strands and buried residues. Validation on a previously published independent dataset shows that NeEMO has a Pearson correlation coefficient of 0.77 and a standard error of 1 Kcal/mol, outperforming nine recent methods. The NeEMO web server can be freely accessed from URL: http://protein.bio.unipd.it/neemo/. Conclusions NeEMO offers an innovative and reliable tool for the annotation of amino acid changes. A key contribution are RINs, which can be used for modeling proteins and their interactions effectively. Interestingly, the approach is very general, and can motivate the development of a new family of RIN-based protein structure analyzers. NeEMO may suggest innovative strategies for bioinformatics tools beyond protein stability prediction. PMID:25057121

  6. Distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of three distal mutants.

    PubMed Central

    Jewsbury, P; Kitagawa, T

    1995-01-01

    Six 90-ps molecular dynamics trajectories, two for each of three distal mutants of sperm whale carbonmonoxy myoglobin, are reported; solvent waters within 16 A of the active site have been included. In both His64GIn trajectories, the distal side chain remains part of the heme pocket, forming a "closed" conformation similar to that of the wild type 64N delta H tautomer. Despite a connectivity more closely resembling the N epsilon H histidine tautomer, close interactions with the carbonyl ligand similar to those observed for the wild type 64N epsilon H tautomer are prevented in this mutant by repulsive interactions between the carbonyl O and the 64O epsilon. The aliphatic distal side chain of the His64Leu mutant shows little interaction with the carbonyl ligand in either His64Leu trajectory. Solvent water molecules move into and out of the active site in the His64Gly mutant trajectories; during all the other carbonmonoxy myoglobin trajectories, including the wild type distal tautomers considered in an earlier work, solvent molecules rarely encroach closer than 6 A of the active site. These results are consistent with a recent structural interpretation of the wild type infrared spectrum, and the current reinterpretation that the distal-ligand interaction in carbonmonoxy myoglobin is largely electrostatic, not steric, in nature. Images FIGURE 5 FIGURE 7 PMID:7787018

  7. Towards numerically robust multireference theories: The driven similarity renormalization group truncated to one- and two-body operators.

    PubMed

    Li, Chenyang; Evangelista, Francesco A

    2016-04-28

    The first nonperturbative version of the multireference driven similarity renormalization group (MR-DSRG) theory [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)] is introduced. The renormalization group structure of the MR-DSRG equations ensures numerical robustness and avoidance of the intruder-state problem, while the connected nature of the amplitude and energy equations guarantees size consistency and extensivity. We approximate the MR-DSRG equations by keeping only one- and two-body operators and using a linearized recursive commutator approximation of the Baker-Campbell-Hausdorff expansion [T. Yanai and G. K.-L. Chan, J. Chem. Phys. 124, 194106 (2006)]. The resulting linearized MR-DSRG scheme with one- and two-body operators [MR-LDSRG(2)] contains only 39 terms and scales as O(N(2)NP (2)NH (2)) where NH, NP, and N correspond to the number of hole, particle, and total orbitals, respectively. Benchmark MR-LDSRG(2) computations on the hydrogen fluoride and molecular nitrogen binding curves and the singlet-triplet splitting of p-benzyne yield results comparable in accuracy to those from multireference configuration interaction, Mukherjee multireference coupled cluster theory, and internally contracted multireference coupled cluster theory. PMID:27131538

  8. Towards numerically robust multireference theories: The driven similarity renormalization group truncated to one- and two-body operators

    NASA Astrophysics Data System (ADS)

    Li, Chenyang; Evangelista, Francesco A.

    2016-04-01

    The first nonperturbative version of the multireference driven similarity renormalization group (MR-DSRG) theory [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)] is introduced. The renormalization group structure of the MR-DSRG equations ensures numerical robustness and avoidance of the intruder-state problem, while the connected nature of the amplitude and energy equations guarantees size consistency and extensivity. We approximate the MR-DSRG equations by keeping only one- and two-body operators and using a linearized recursive commutator approximation of the Baker-Campbell-Hausdorff expansion [T. Yanai and G. K.-L. Chan, J. Chem. Phys. 124, 194106 (2006)]. The resulting linearized MR-DSRG scheme with one- and two-body operators [MR-LDSRG(2)] contains only 39 terms and scales as O ( N 2 NP 2 NH 2 ) where NH, NP, and N correspond to the number of hole, particle, and total orbitals, respectively. Benchmark MR-LDSRG(2) computations on the hydrogen fluoride and molecular nitrogen binding curves and the singlet-triplet splitting of p-benzyne yield results comparable in accuracy to those from multireference configuration interaction, Mukherjee multireference coupled cluster theory, and internally contracted multireference coupled cluster theory.

  9. PTPRT regulates the interaction of Syntaxin-binding protein 1 with Syntaxin 1 through dephosphorylation of specific tyrosine residue

    SciTech Connect

    Lim, So-Hee; Moon, Jeonghee; Lee, Myungkyu; Lee, Jae-Ran

    2013-09-13

    Highlights: •PTPRT is a brain-specific, expressed, protein tyrosine phosphatase. •PTPRT regulated the interaction of Syntaxin-binding protein 1 with Syntaxin 1. •PTPRT dephosphorylated the specific tyrosine residue of Syntaxin-binding protein 1. •Dephosphorylation of Syntaxin-binding protein 1 enhanced the interaction with Syntaxin 1. •PTPRT appears to regulate the fusion of synaptic vesicle through dephosphorylation. -- Abstract: PTPRT (protein tyrosine phosphatase receptor T), a brain-specific tyrosine phosphatase, has been found to regulate synaptic formation and development of hippocampal neurons, but its regulation mechanism is not yet fully understood. Here, Syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, was identified as a possible interaction partner and an endogenous substrate of PTPRT. PTPRT interacted with Syntaxin-binding protein 1 in rat synaptosome, and co-localized with Syntaxin-binding protein 1 in cultured hippocampal neurons. PTPRT dephosphorylated tyrosine 145 located around the linker between domain 1 and 2 of Syntaxin-binding protein 1. Syntaxin-binding protein 1 directly binds to Syntaxin 1, a t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein, and plays a role as catalysts of SNARE complex formation. Syntaxin-binding protein 1 mutant mimicking non-phosphorylation (Y145F) enhanced the interaction with Syntaxin 1 compared to wild type, and therefore, dephosphorylation of Syntaxin-binding protein 1 appeared to be important for SNARE-complex formation. In conclusion, PTPRT could regulate the interaction of Syntaxin-binding protein 1 with Syntaxin 1, and as a result, the synaptic vesicle fusion appeared to be controlled through dephosphorylation of Syntaxin-binding protein 1.

  10. Two-body correlations and natural-orbital tomography in ultracold bosonic systems of definite parity

    NASA Astrophysics Data System (ADS)

    Kroenke, Sven; Schmelcher, Peter

    2016-05-01

    Deep insights into the structure of a many-body state can often be inferred from its natural orbitals (eigenvectors of the reduced one-body density operator) and their populations. These quantities allow e.g. to distinguish a Bose-Einstein condensate from a correlated many-body state and were utilized to understand many-body processes such as the decay of dark solitons due to dynamical quantum depletion. We explore the relationship between natural orbitals, one-body coherences and two-body correlations for a certain important class of bosonic many-body wave-functions with definite parity. The strength of two-body correlations at the parity-symmetry center is shown (i) to characterize the number state distribution and (ii) to control the structure of non-local two-body correlations. A recipe for the experimental reconstruction of the natural-orbital densities based on two-body correlation measurements is derived. These results are applied to decaying dark solitons.

  11. Universal algorithms and programs for calculating the motion parameters in the two-body problem

    NASA Technical Reports Server (NTRS)

    Bakhshiyan, B. T.; Sukhanov, A. A.

    1979-01-01

    The algorithms and FORTRAN programs for computing positions and velocities, orbital elements and first and second partial derivatives in the two-body problem are presented. The algorithms are applicable for any value of eccentricity and are convenient for computing various navigation parameters.

  12. Singularity in the Laboratory Frame Angular Distribution Derived in Two-Body Scattering Theory

    ERIC Educational Resources Information Center

    Dick, Frank; Norbury, John W.

    2009-01-01

    The laboratory (lab) frame angular distribution derived in two-body scattering theory exhibits a singularity at the maximum lab scattering angle. The singularity appears in the kinematic factor that transforms the centre of momentum (cm) angular distribution to the lab angular distribution. We show that it is caused in the transformation by the…

  13. Two-body Relaxation Driven Evolution of the Young Stellar Disk in the Galactic Center

    NASA Astrophysics Data System (ADS)

    Šubr, Ladislav; Haas, Jaroslav

    2014-05-01

    The center of our Galaxy hosts almost two hundred very young stars, a subset of which is orbiting the central supermassive black hole (SMBH) in a relatively thin disk-like structure. First analyses indicated a power-law surface density profile of the disk, ΣvpropR β with β = -2. Recently, however, doubts about this profile arose. In particular, it now seems to be better described by a sort of broken power law. By means of both analytical arguments and numerical N-body modeling, we show that such a broken power-law profile is a natural consequence of the two-body relaxation of the disk. Due to the small relative velocities of the nearby stars in co-planar Keplerian orbits around the SMBH, two-body relaxation is effective enough to affect the evolution of the disk on timescales comparable to its estimated age. In the inner, densest part of the disk, the profile becomes rather flat (β ≈ -1) while the outer parts keep imprints of the initial state. Our numerical models show that the observed projected surface density profile of the young stellar disk can result from two-body relaxation driven evolution of a disk with initial single power-law profile with -2 <~ β <~ -1.5. In addition, we suggest that two-body relaxation may have caused a significant radial migration of the S-stars toward the central SMBH, thus playing an important role in their formation scenario.

  14. Experiments driving theory: Gravitational wave detection and the two body problem in general relativity

    NASA Astrophysics Data System (ADS)

    Iyer, Bala R.

    2016-05-01

    Over the last two decades, the search for gravitational waves from coalescing compact binaries by detectors like LIGO and Virgo has crucially required and consequently spurred tremendous progress in the two body problem in general relativity. A broad brush overview of these major developments and the current status of these significant results is presented.

  15. Selective determination of thiram residues in fruit and vegetables by hydrophilic interaction LC-MS.

    PubMed

    Ringli, Daniela; Schwack, Wolfgang

    2013-01-01

    Thiram belongs to the most important class of dithiocarbamate (DTC) fungicides including dimethyldithiocarbamates (DMDs), ethylenebis(dithiocarbamtes) (EBDs) and propylenebis(dithiocarbamates) (PBDs). During the surface extraction of fruit and vegetables for the LC-MS determination of residues of DMDs, EBDs and PBDs, thiram is reduced by the penicillamine buffer to the DMD anion, thus resulting in false-positive findings of DMD fungicides like ziram. Therefore, an alkaline sulfite buffer was applied for surface extraction, quantitatively transforming thiram into the DMD anion and a stable DMD-sulfite adduct that was used as a selective marker for thiram. Separation was performed isocratically on a ZIC-pHILIC column with acetonitrile-10 mM ammonium hydroxide solution (85/15). Mass selective detection was carried out on a single-quadrupole mass spectrometer coupled to an electrospray ionisation interface operating in negative mode. Using d12-thiram as the internal standard, recoveries of 80-108% were obtained from apples, tomatoes, grapes and sweet peppers, spiked in the range of 0.02-1 mg kg(-1). Limits of detection and quantification were 0.6 and 2 µg kg(-1), respectively. PMID:24070320

  16. Fujiwhara interaction of tropical cyclone scale vortices using a weighted residual collocation method

    NASA Astrophysics Data System (ADS)

    Walsh, Raymond P.; Alam, Jahrul M.

    2016-09-01

    The fundamental interaction between tropical cyclones was investigated through a series of water tank experiements by Fujiwhara [20, 21, 22]. However, a complete understanding of tropical cyclones remains an open research challenge although there have been numerous investigations through measurments with aircrafts/satellites, as well as with numerical simulations. This article presents a computational model for simulating the interaction between cyclones. The proposed numerical method is presented briefly, where the time integration is performed by projecting the discrete system onto a Krylov subspace. The method filters the large scale fluid dynamics using a multiresolution approximation, and the unresolved dynamics is modeled with a Smagorinsky type subgrid scale parameterization scheme. Numerical experiments with Fujiwhara interactions are considered to verify modeling accuracy. An excellent agreement between the present simulation and a reference simulation at Re = 5000 has been demonstrated. At Re = 37440, the kinetic energy of cyclones is seen consolidated into larger scales with concurrent enstrophy cascade, suggesting a steady increase of energy containing scales, a phenomena that is typical in two-dimensional turbulence theory. The primary results of this article suggest a novel avenue for addressing some of the computational challenges of mesoscale atmospheric circulations.

  17. Tyrosine residues 654 and 670 in {beta}-cat enin are crucial in regulation of Met-{beta}-catenin interactions

    SciTech Connect

    Zeng, Gang; Apte, Udayan; Micsenyi, Amanda; Bell, Aaron; Monga, Satdarshan P.S. . E-mail: smonga@pitt.edu

    2006-11-01

    {beta}-catenin, a key component of the canonical Wnt pathway, is also regulated by tyrosine phosphorylation that regulates its association to E-cadherin. Previously, we reported its association with the hepatocyte growth factor (HGF) receptor Met at the membrane. HGF induced Met-{beta}-catenin dissociation and nuclear translocation of {beta}-catenin, which was tyrosine-phosphorylation-dependent. Here, we further investigate the Met-{beta}-catenin interaction by selectively mutating several tyrosine residues, alone or in combination, in {beta}-catenin. The mutants were subcloned into FLAG-CMV vector and stably transfected into rat hepatoma cells, which were treated with HGF. All single or double-mutant-transfected cells continued to show HGF-induced nuclear translocation of FLAG-{beta}-catenin except the mutations affecting 654 and 670 simultaneously (Y654/670F), which coincided with the lack of formation of {beta}-catenin-TCF complex and DNA synthesis, in response to the HGF treatment. In addition, the Y654/670F-transfected cells also showed no phosphorylation of {beta}-catenin or dissociation from Met in response to HGF. Thus, intact 654 and 670 tyrosine residues in {beta}-catenin are crucial in HGF-mediated {beta}-catenin translocation, activation and mitogenesis.

  18. Structure-function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin

    SciTech Connect

    Mogi, T.; Marti, T.; Khorana, H.G. )

    1989-08-25

    Bacteriorhodopsin contains 8 tryptophan residues distributed across the membrane-embedded helices. To study their possible functions, we have replaced them one at a time by phenylalanine; in addition, Trp-137 and -138 have been replaced by cysteine. The mutants were prepared by cassette mutagenesis of the synthetic bacterio-opsin gene, expression and purification of the mutant apoproteins, renaturation, and chromophore regeneration. The replacement of Trp-10, Trp-12 (helix A), Trp-80 (helix C), and Trp-138 (helix E) by phenylalanine and of Trp-137 and Trp-138 by cysteine did not significantly alter the absorption spectra or affect their proton pumping. However, substitution of the remaining tryptophans by phenylalanine had the following effects. (1) Substitution of Trp-86 (helix C) and Trp-137 gave chromophores blue-shifted by 20 nm and resulted in reduced proton pumping to about 30%. (2) As also reported previously, substitution of Trp-182 and Trp-189 (helix F) caused large blue shifts (70 and 40 nm, respectively) in the chromophore and affected proton pumping. (3) The substitution of Trp-86 and Trp-182 by phenylalanine conferred acid instability on these mutants. The spectral shifts indicate that Trp-86, Trp-182, Trp-189, and possibly Trp-137 interact with retinal. It is proposed that these tryptophans, probably along with Tyr-57 (helix B) and Tyr-185 (helix F), form a retinal binding pocket. We discuss the role of tryptophan residues that are conserved in bacteriorhodopsin, halorhodopsin, and the related family of opsin proteins.

  19. Two Arginine Residues of Streptococcus gordonii Sialic Acid-Binding Adhesin Hsa Are Essential for Interaction to Host Cell Receptors

    PubMed Central

    Urano-Tashiro, Yumiko; Takahashi, Yukihiro; Oguchi, Riyo; Konishi, Kiyoshi

    2016-01-01

    Hsa is a large, serine-rich protein of Streptococcus gordonii DL1 that mediates binding to α2-3-linked sialic acid termini of glycoproteins, including platelet glycoprotein Ibα, and erythrocyte membrane protein glycophorin A, and band 3. The binding of Hsa to platelet glycoprotein Ibα contributes to the pathogenesis of infective endocarditis. This interaction appears to be mediated by a second non-repetitive region (NR2) of Hsa. However, the molecular details of the interaction between the Hsa NR2 region and these glycoproteins are not well understood. In the present study, we identified the amino acid residues of the Hsa NR2 region that are involved in sialic acid recognition. To identify the sialic acid-binding site of Hsa NR2 region, we prepared various mutants of Hsa NR2 fused with glutathione transferase. Fusion proteins harboring Arg340 to Asn (R340N) or Arg365 to Asn (R365N) substitutions in the NR2 domain exhibited significantly reduced binding to human erythrocytes and platelets. A sugar-binding assay showed that these mutant proteins abolished binding to α2-3-linked sialic acid. Furthermore, we established S. gordonii DL1 derivatives that encoded the corresponding Hsa mutant protein. In whole-cell assays, these mutant strains showed significant reductions in hemagglutination, in platelet aggregation, and in adhesion to human leukocytes. These results indicate that the Arg340 and Arg365 residues of Hsa play an important role in the binding of Hsa to α2-3-linked sialic acid-containing glycoproteins. PMID:27101147

  20. Two Arginine Residues of Streptococcus gordonii Sialic Acid-Binding Adhesin Hsa Are Essential for Interaction to Host Cell Receptors.

    PubMed

    Urano-Tashiro, Yumiko; Takahashi, Yukihiro; Oguchi, Riyo; Konishi, Kiyoshi

    2016-01-01

    Hsa is a large, serine-rich protein of Streptococcus gordonii DL1 that mediates binding to α2-3-linked sialic acid termini of glycoproteins, including platelet glycoprotein Ibα, and erythrocyte membrane protein glycophorin A, and band 3. The binding of Hsa to platelet glycoprotein Ibα contributes to the pathogenesis of infective endocarditis. This interaction appears to be mediated by a second non-repetitive region (NR2) of Hsa. However, the molecular details of the interaction between the Hsa NR2 region and these glycoproteins are not well understood. In the present study, we identified the amino acid residues of the Hsa NR2 region that are involved in sialic acid recognition. To identify the sialic acid-binding site of Hsa NR2 region, we prepared various mutants of Hsa NR2 fused with glutathione transferase. Fusion proteins harboring Arg340 to Asn (R340N) or Arg365 to Asn (R365N) substitutions in the NR2 domain exhibited significantly reduced binding to human erythrocytes and platelets. A sugar-binding assay showed that these mutant proteins abolished binding to α2-3-linked sialic acid. Furthermore, we established S. gordonii DL1 derivatives that encoded the corresponding Hsa mutant protein. In whole-cell assays, these mutant strains showed significant reductions in hemagglutination, in platelet aggregation, and in adhesion to human leukocytes. These results indicate that the Arg340 and Arg365 residues of Hsa play an important role in the binding of Hsa to α2-3-linked sialic acid-containing glycoproteins. PMID:27101147

  1. Validation of Proposed Metrics for Two-Body Abrasion Scratch Test Analysis Standards

    NASA Technical Reports Server (NTRS)

    Street, Kenneth W., Jr.; Kobrick, Ryan L.; Klaus, David M.

    2013-01-01

    Abrasion of mechanical components and fabrics by soil on Earth is typically minimized by the effects of atmosphere and water. Potentially abrasive particles lose sharp and pointed geometrical features through erosion. In environments where such erosion does not exist, such as the vacuum of the Moon, particles retain sharp geometries associated with fracturing of their parent particles by micrometeorite impacts. The relationship between hardness of the abrasive and that of the material being abraded is well understood, such that the abrasive ability of a material can be estimated as a function of the ratio of the hardness of the two interacting materials. Knowing the abrasive nature of an environment (abrasive)/construction material is crucial to designing durable equipment for use in such surroundings. The objective of this work was to evaluate a set of standardized metrics proposed for characterizing a surface that has been scratched from a two-body abrasion test. This is achieved by defining a new abrasion region termed Zone of Interaction (ZOI). The ZOI describes the full surface profile of all peaks and valleys, rather than just measuring a scratch width. The ZOI has been found to be at least twice the size of a standard width measurement; in some cases, considerably greater, indicating that at least half of the disturbed surface area would be neglected without this insight. The ZOI is used to calculate a more robust data set of volume measurements that can be used to computationally reconstruct a resultant profile for de tailed analysis. Documenting additional changes to various surface roughness par ameters also allows key material attributes of importance to ultimate design applications to be quantified, such as depth of penetration and final abraded surface roughness. Further - more, by investigating the use of custom scratch tips for specific needs, the usefulness of having an abrasion metric that can measure the displaced volume in this standardized

  2. Systematics of the release of residual nuclei from relativistic nucleus-nucleus interactions

    NASA Technical Reports Server (NTRS)

    Binns, W. R.; Israel, M. H.; Klarmann, J.; Garrard, T. L.; Kertzmann, M. P.

    1987-01-01

    Relativistic nuclei of krypton, xenon, holmium, and gold, accelerated in a partially stripped state to a maximum rigidity of about 5.6 GeV, interacting with targets of aluminum, carbon, and polyethylene are examined. For each projectile and target combination, determinations are made for the total and partial charge changing cross sections for the production of lighter fragments. From these measurements, a new representation of the dependence of the total charge changing cross sections on beam and target charge is developed. Simple representations of the variation of the partial cross sections were identified with the charge of the produced fragments and shown to be dependent on the charge and energy of the beam. The fission of gold nuclei at high energies in these various targets has also been studied.

  3. Systematics of the release of residual nuclei from relativistic nucleus-nucleus interactions

    SciTech Connect

    Binns, W.R.; Garrard, T.L.; Israel, M.H.; Kertzmann, M.P.; Klarmann, J.; Stone, E.C.; Waddington, C.J.

    1987-11-01

    We have examined relativistic nuclei of krypton, xenon, holmium, and gold, accelerated in a partially stripped state to a maximum rigidity of about 5.6 GeV, interacting with targets of aluminum, carbon, and polyethylene. For each projectile and target combination we determined the total and partial charge changing cross sections for the production of lighter fragments. From these measurements we have developed a new representation of the dependence of the total charge changing cross sections on beam and target charge. We have also identified simple representations of the variation of the partial cross sections with the charge of the produced fragments and shown that they are dependent on the charge and energy of the beam. The fission of gold nuclei at high energies in these various targets has also been studied.

  4. Number of Sialic Acid Residues in Ganglioside Headgroup Affects Interactions with Neighboring Lipids

    PubMed Central

    Frey, Shelli L.; Lee, Ka Yee C.

    2013-01-01

    Monolayers of binary mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and asialo-(GA1), disialo-(GD1b) and trisialo-(GT1b) gangliosides were used to determine the effect of ganglioside headgroup charge and geometry on its interactions with the neighboring zwitterionic lipid. Surface pressure versus molecular area isotherm measurements along with concurrent fluorescence microscopy of the monolayers at the air-water interface were complemented with atomic force microscopy imaging of monolayers deposited on solid substrates. Results were used to further develop a proposed geometric packing model that the complementary geometry of DPPC and monosialoganglioside GM1 headgroups affects their close molecular packing, inducing condensation of the layer at small mol % of ganglioside. For GA1, GD1b, and GT1b, a similar condensing effect, followed by a fluidizing effect is seen that varies with glycosphingolipid concentration, but results do not directly follow from geometric arguments because less DPPC is needed to condense ganglioside molecules with larger cross-sectional areas. The variations in critical packing mole ratios can be explained by global effects of headgroup charge and resultant dipole moments within the monolayer. Atomic force microscopy micrographs further support the model of ganglioside-induced DPPC condensation with condensed domains composed of a striped phase of condensed DPPC and DPPC/ganglioside geometrically packed complexes at low concentrations. PMID:24047994

  5. Number of sialic acid residues in ganglioside headgroup affects interactions with neighboring lipids.

    PubMed

    Frey, Shelli L; Lee, Ka Yee C

    2013-09-17

    Monolayers of binary mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and asialo-(GA1), disialo-(GD1b) and trisialo-(GT1b) gangliosides were used to determine the effect of ganglioside headgroup charge and geometry on its interactions with the neighboring zwitterionic lipid. Surface pressure versus molecular area isotherm measurements along with concurrent fluorescence microscopy of the monolayers at the air-water interface were complemented with atomic force microscopy imaging of monolayers deposited on solid substrates. Results were used to further develop a proposed geometric packing model that the complementary geometry of DPPC and monosialoganglioside GM1 headgroups affects their close molecular packing, inducing condensation of the layer at small mol % of ganglioside. For GA1, GD1b, and GT1b, a similar condensing effect, followed by a fluidizing effect is seen that varies with glycosphingolipid concentration, but results do not directly follow from geometric arguments because less DPPC is needed to condense ganglioside molecules with larger cross-sectional areas. The variations in critical packing mole ratios can be explained by global effects of headgroup charge and resultant dipole moments within the monolayer. Atomic force microscopy micrographs further support the model of ganglioside-induced DPPC condensation with condensed domains composed of a striped phase of condensed DPPC and DPPC/ganglioside geometrically packed complexes at low concentrations. PMID:24047994

  6. Two-body physics in quasi-low-dimensional atomic gases under spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Wang, Jing-Kun; Yi, Wei; Zhang, Wei

    2016-06-01

    One of the most dynamic directions in ultracold atomic gas research is the study of low-dimensional physics in quasi-low-dimensional geometries, where atoms are confined in strongly anisotropic traps. Recently, interest has significantly intensified with the realization of synthetic spin-orbit coupling (SOC). As a first step toward understanding the SOC effect in quasi-low-dimensional systems, the solution of two-body problems in different trapping geometries and different types of SOC has attracted great attention in the past few years. In this review, we discuss both the scattering-state and the bound-state solutions of two-body problems in quasi-one and quasi-two dimensions. We show that the degrees of freedom in tightly confined dimensions, in particular with the presence of SOC, may significantly affect system properties. Specifically, in a quasi-one-dimensional atomic gas, a one-dimensional SOC can shift the positions of confinement-induced resonances whereas, in quasitwo- dimensional gases, a Rashba-type SOC tends to increase the two-body binding energy, such that more excited states in the tightly confined direction are occupied and the system is driven further away from a purely two-dimensional gas. The effects of the excited states can be incorporated by adopting an effective low-dimensional Hamiltonian having the form of a two-channel model. With the bare parameters fixed by two-body solutions, this effective Hamiltonian leads to qualitatively different many-body properties compared to a purely low-dimensional model.

  7. Two-body relaxation driven evolution of the young stellar disk in the galactic center

    SciTech Connect

    Šubr, Ladislav; Haas, Jaroslav

    2014-05-10

    The center of our Galaxy hosts almost two hundred very young stars, a subset of which is orbiting the central supermassive black hole (SMBH) in a relatively thin disk-like structure. First analyses indicated a power-law surface density profile of the disk, Σ∝R {sup β} with β = –2. Recently, however, doubts about this profile arose. In particular, it now seems to be better described by a sort of broken power law. By means of both analytical arguments and numerical N-body modeling, we show that such a broken power-law profile is a natural consequence of the two-body relaxation of the disk. Due to the small relative velocities of the nearby stars in co-planar Keplerian orbits around the SMBH, two-body relaxation is effective enough to affect the evolution of the disk on timescales comparable to its estimated age. In the inner, densest part of the disk, the profile becomes rather flat (β ≈ –1) while the outer parts keep imprints of the initial state. Our numerical models show that the observed projected surface density profile of the young stellar disk can result from two-body relaxation driven evolution of a disk with initial single power-law profile with –2 ≲ β ≲ –1.5. In addition, we suggest that two-body relaxation may have caused a significant radial migration of the S-stars toward the central SMBH, thus playing an important role in their formation scenario.

  8. Integrals of motion for the classical two-body problem with drag

    NASA Technical Reports Server (NTRS)

    Jezewski, D. J.; Mittleman, D.

    1983-01-01

    Integrals of motion for the two-body problem with drag are obtained by operating on the second-order vector differential equation describing the motion. The force field consists of an inverse-square gravitational attraction and a drag force proportional to the velocity vector and inversely proportional to the square of the distance to the attracting center. The developed integrals are the analogs of the Keplerian scalar energy, the vector angular momentum, and the Laplace vector.

  9. Specific Inter-residue Interactions as Determinants of Human Monoacylglycerol Lipase Catalytic Competency: A ROLE FOR GLOBAL CONFORMATIONAL CHANGES.

    PubMed

    Tyukhtenko, Sergiy; Karageorgos, Ioannis; Rajarshi, Girija; Zvonok, Nikolai; Pavlopoulos, Spiro; Janero, David R; Makriyannis, Alexandros

    2016-02-01

    The serine hydrolase monoacylglycerol lipase (MGL) functions as the main metabolizing enzyme of 2-arachidonoyl glycerol, an endocannabinoid signaling lipid whose elevation through genetic or pharmacological MGL ablation exerts therapeutic effects in various preclinical disease models. To inform structure-based MGL inhibitor design, we report the direct NMR detection of a reversible equilibrium between active and inactive states of human MGL (hMGL) that is slow on the NMR time scale and can be modulated in a controlled manner by pH, temperature, and select point mutations. Kinetic measurements revealed that hMGL substrate turnover is rate-limited across this equilibrium. We identify a network of aromatic interactions and hydrogen bonds that regulates hMGL active-inactive state interconversion. The data highlight specific inter-residue interactions within hMGL modulating the enzymes function and implicate transitions between active (open) and inactive (closed) states of the hMGL lid domain in controlling substrate access to the enzymes active site. PMID:26555264

  10. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin, 1998 Annual Report.

    SciTech Connect

    James, Brenda B.; Pearsons, Todd N.; McMichael, Geoffrey A.

    1999-12-01

    Select ecological interactions and spring chinook salmon residual/precocial abundance were monitored in 1998 as part of the Yakima/Klickitat Fisheries Project's supplementation monitoring program. Monitoring these variables is part of an effort to help evaluate the factors that contribute to, or limit supplementation success. The ecological interactions that were monitored were prey consumption, competition for food, and competition for space. The abundance of spring chinook salmon life-history forms that have the potential to be influenced by supplementation and that have important ecological and genetic roles were monitored (residuals and precocials). Residual spring chinook salmon do not migrate to the ocean during the normal emigration period and continue to rear in freshwater. Precocials are those salmon that precocially mature in freshwater. The purpose of sampling during 1998 was to collect baseline data one year prior to the release of hatchery spring chinook salmon which occurred during the spring of 1999. All sampling that the authors report on here was conducted in upper Yakima River during summer and fall 1998. The stomach fullness of juvenile spring chinook salmon during the summer and fall averaged 12%. The food competition index suggested that mountain whitefish (0.59), rainbow trout (0.55), and redside shiner (0.55) were competing for food with spring chinook salmon. The space competition index suggested that rainbow trout (0.31) and redside shiner (0.39) were competing for space with spring chinook salmon but mountain whitefish (0.05) were not. Age-0 spring chinook salmon selected a fairly narrow range of microhabitat parameters in the summer and fall relative to what was available. Mean focal depths and velocities for age 0 spring chinook salmon during the summer were 0.5 m {+-} 0.2 m and 0.26 m/s {+-} 0.19 m/s, and during the fall 0.5 m {+-} 0.2 m and 0.24 m/s {+-} 0.18 m/s. Among potential competitors, age 1+ rainbow trout exhibited the greatest

  11. The distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of two distal histidine tautomers.

    PubMed Central

    Jewsbury, P; Kitagawa, T

    1994-01-01

    Four independent 90 ps molecular dynamics simulations of sperm-whale wild-type carbonmonoxy myoglobin (MbCO) have been calculated using a new AMBER force field for the haem prosthetic group. Two trajectories have the distal 64N delta nitrogen protonated, and two have the 64N epsilon nitrogen protonated; all water molecules within 16 A of the carbonyl O are included. In three trajectories, the distal residue remains part of the haem pocket, with the protonated distal nitrogen pointing into the active site. This is in contrast with the neutron diffraction crystal structure, but is consistent with the solution phase CO stretching frequencies (upsilon CO) of MbCO and various of its mutants. There are significant differences in the "closed" pocket structures found for each tautomer: the 64N epsilon H trajectories both show stable distal-CO interactions, whereas the 64N delta H tautomer) has a weaker interaction resulting in a more mobile distal side chain. One trajectory (a 64N delta H tautomer) has the distal histidine moving out into the "solvent", leaving the pocket in an "open" structure, with a large unhindered entrance to the active site. These trajectories suggest that the three upsilon CO frequencies observed for wild-type MbCO in solution, rather than representing significantly different Fe-C-O geometries as such, arise from three different haem pocket structures, each with different electric fields at the ligand. Each pocket structure corresponds to a different distal histidine conformer: the A3 band to the 64N epsilon H tautomer, the A1,2 band to the 64N delta H tautomer, and the A0 band to the absence of any significant interaction with the distal side chain. PMID:7696465

  12. Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex.

    PubMed

    You, Zhiying; Ode, Koji L; Shindo, Mayumi; Takisawa, Haruhiko; Masai, Hisao

    2016-05-01

    All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in Xenopus egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity. PMID:26940553

  13. Carboxymethylation of methionine residues in bovine pituitary luteinizing hormone and its subunits. Effects on the binding activity with receptor sites and interactions between subunits.

    PubMed Central

    Cheng, K W

    1976-01-01

    The reaction of iodoacetic acid with bovine lutropin (luteinizing hormone) at pH 3.0 was specific for methionine residues; it was slow and reached its equilibrium after 12 h at 37 degrees C. The number of modified methionine residues increased proportionately with the amount of the alkylating reagent in the reaction mixture. In the presence of a 20-fold molar excess of iodoacetic acid with respect to methionine, essentially all methionine residues in both subunits of bovine lutropin were carboxymethylated. Studies of various recombinations of modified and native alpha and beta subunits showed that methionine residues in bovine lutropin were not essential for interactions between subunits. Various recombinants were characterized by polyacrylamide-gel electrophoresis and gel filtration of Sephadex G-100. Immunological cross-reactivity by radioimmunoassay of the recombinants of modified alpha and beta subunits was relatively similar to that of the native subunits. However, the biological activity measured by receptor-site binding of the recombinants of alpha and beta chains with a total of three alkylated methionine residues was less than 5% of the activity of native lutropin. It is noteworthy that recombinants of a modified subunit and a native counterpart subunit regenerated 20-30 % of biological activity. These findings suggested that at least 1-2 methionine residues in each subunit are involved in the hormone-receptor interaction for bovine lutropin. Images PLATE 1 PMID:187169

  14. Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qbeta replicase efficiently binds small RNAs by recognizing pyrimidine residues.

    PubMed

    Preuss, R; Dapprich, J; Walter, N G

    1997-10-31

    Binding of small RNAs by the RNA-dependent RNA polymerase of coliphage Qbeta was studied utilizing a fluorometric assay. A DNA oligonucleotide probe of sequence 5'-d(TTTTTCC) was 5'-end-labeled with pyrene. In this construct, the proximal thymine residues efficiently quench the fluorophore emission in solution. Upon stoichiometric binding of one probe per polymerase molecule, the pyrene steady-state fluorescence increases by two orders of magnitude, the fluorescence anisotropy increases, and a long fluorescence lifetime component of 140 ns appears. With addition of replicable RNA, steady-state fluorescence decreases in a concentration dependent manner and the long lifetime component is lost. This observation most likely reflects displacement of the pyrene-labeled probe from the proposed nucleic acid binding site II of Qbeta replicase. The effect was utilized to access binding affinities of different RNAs to this site in a reverse titration assay format. In 10 mM sodium phosphate (pH 7.0), 100 mM NaCl, at 16 degrees C, equilibrium dissociation constants for different template midi- and minivariant RNAs were calculated to be in the nanomolar range. In general, the minus and plus strands, concomitantly synthesized by Qbeta replicase during replication, exhibited discriminative affinities, while their hybrid bound less efficiently than either of the single strands. Different non-replicable tRNAs also bound to the polymerase with comparable dissociation constants. By titration with DNA homo-oligonucleotides it was shown that the probed site on Qbeta replicase does not require a 2' hydroxyl group for binding nucleic acids, but recognizes pyrimidine residues. Its interaction with thymine is lost in an A.T base-pair, while that with cytosine is retained after Watson-Crick base-pairing. These findings can explain the affinities of RNA-Qbeta replicase interactions reported here and in earlier investigations. The sensitivity of the described fluorometric assay allows

  15. Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

    PubMed

    Kuo, Hsiou-Ting; Liu, Shing-Lung; Chiu, Wen-Chieh; Fang, Chun-Jen; Chang, Hsien-Chen; Wang, Wei-Ren; Yang, Po-An; Li, Jhe-Hao; Huang, Shing-Jong; Huang, Shou-Ling; Cheng, Richard P

    2015-05-01

    β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif. PMID:25646959

  16. Low-energy structure studies of odd-odd deformed nuclei and the coriolis and residual interactions

    SciTech Connect

    Dewberry, R.A.

    1980-08-01

    The nuclear level structure of /sup 176/Lu, /sup 170/Tm, /sup 166/Ho, and /sup 160/Tb have been studied by means of the /sup 177/Hf(t,..cap alpha..)/sup 176/Lu, /sup 171/Yb(t,..cap alpha..)/sup 170/Tm, /sup 167/Er(t,..cap alpha..)/sup 166/Ho, and /sup 161/Dy(t,..cap alpha..)/sup 160/Tb reactions and with the use of previously published (d,p) spectroscopy and gamma transitions from the (n,..gamma..) reactions. The (t,..cap alpha..) reactions have been performed and analyzed with 17 MeV tritons and the Los Alamos Q3D spectrometer. Eighty-one new rotational states in excited proton configurations or vibrational excited states are proposed. An independent parameterization of the Coriolis interaction is presented, which leads to satisfactory results in reproducing experimental single-particle transfer reaction cross-sections by theoretical calculations. The anomalous population of the excited neutron configurations (404 reduces to -624 up arrow) in /sup 176/Lu and (411 reduces to +- 512 up arrow) in /sup 170/Tm, and the anomalously low (t,..cap alpha..) cross-sections of the (411 up arrow +- 633 up arrow) configuration in /sup 166/Ho are observed. Qualitative explanation of the anomalies is presented in terms of the mixing of states which satisfy the requirement delta/sub I'/,/sub I/delta/sub K'/,/sub K/. Off-diagonal H/sub INT/ matrix elements are calculated, which show that the residual interaction cannot be used to account for the magnitude of the cross-sections observed.

  17. Identification of residues crucial for the interaction between human neuroglobin and the α-subunit of heterotrimeric Gi protein

    PubMed Central

    Takahashi, Nozomu; Wakasugi, Keisuke

    2016-01-01

    Mammalian neuroglobin (Ngb) protects neuronal cells under conditions of oxidative stress. We previously showed that human Ngb acts as a guanine nucleotide dissociation inhibitor (GDI) for the α-subunits of heterotrimeric Gi/o proteins and inhibits the decrease in cAMP concentration, leading to protection against cell death. In the present study, we used an eukaryotic expression vector driving high-level expression of human wild-type Ngb or Ngb mutants that either exhibit or lack GDI activities in human cells. We demonstrate that the GDI activity of human Ngb is tightly correlated with its neuroprotective activity. We further demonstrate that Glu53, Glu60, and Glu118 of human Ngb are crucial for both the neuroprotective activity and interaction with Gαi1. Moreover, we show that Lys46, Lys70, Arg208, Lys209, and Lys210 residues of Gαi1 are important for binding to human Ngb. We propose a molecular docking model of the complex between human Ngb and Gαi1. PMID:27109834

  18. Low oxygen affinity in reptilian hemoglobin D: prediction of residue interactions in Geochelone carbonaria HbD by homology modeling.

    PubMed

    Lutfullah, Ghosia; Khalil, Hilal Shahid; Amin, Farhat; Azhar, Noreen

    2008-04-01

    The homology model of hemoglobin D from Geochelone carbonaria, the red-footed tortoise was predicted using the 3D structure coordinates of Geochelone gigantea hemoglobin D as the template. The model was built using the program, MODELLER (8v1) and evaluated with PROCHECK and PROSA. The present study features an in-depth analysis of the 3D model and its conformational changes brought about with variations in its environment. These structural changes are correlated with its ability to adapt to different environmental constraints enabling the organism to better suit to its natural habitat. The model shows additional contacts between amino acid pairs of alpha-119 and beta-55, alpha-35 and beta-124, alpha-103 and beta-112, alpha-115 and beta-116, alpha-120 and beta-52, alpha-120 and beta-55, alpha-36 and beta-127 which are not found in human hemoglobin. It is predicted that these contacts may result in T-state stabilization thus lowering oxygen affinity. Furthermore, decrease in the interaction of phosphate heteroatoms with the amino acid residues of G. carbonaria Hb was also predicted in this study. PMID:18085430

  19. Simultaneous determination of residues of dipyrone metabolites in goat tissues by hydrophilic interaction liquid chromatography tandem mass spectrometry.

    PubMed

    Zhang, Chong; Zhang, Lifang; Cao, Suqing; Jiang, Zhaoling; Wu, Hao; Yan, Ming; Zhang, Xiaoxiao; Jiang, Shanxiang; Xue, Feiqun

    2016-04-01

    A reliable LC-MS/MS method with high sensitivity was developed and validated for the determination of dipyrone (DIP) metabolites in goat muscle, fat, liver, and kidney samples. Analytes were extracted using acetonitrile mixed with ammonia solution. After dehydration and evaporation to dryness, extracts were purified using an Oasis MAX cartridge. Chromatographic separation was performed on a hydrophilic interaction liquid chromatography column. The analytes were then detected using triple-quadrupole mass spectrometry in positive electrospray ionization and multiple reaction monitoring mode. Calibration plots were constructed using matrix-matched standards and showed good linearity. Limits of quantification for 4-methylaminoantipyrine (MAA), 4-formylaminoantipyrine (FAA), and 4-acetylaminoantipyrone (AAA) ranged from 0.4 μg kg(-1) to 6 μg kg(-1), while those for 4-aminoantipyrone (AA) ranged from 10 μg kg(-1) to 125 μg kg(-1) in all tissues. The developed method was successfully applied in the determination of DIP metabolite residues in actual goat tissues. PMID:26593468

  20. A novel anti-aldolase C antibody specifically interacts with residues 85–102 of the protein

    PubMed Central

    Langellotti, Simona; Romano, Maurizio; Guarnaccia, Corrado; Granata, Vincenzo; Orrù, Stefania; Zagari, Adriana; Baralle, Francisco E; Salvatore, Francesco

    2014-01-01

    Aldolase C is a brain-specific glycolytic isozyme whose complete repertoire of functions are obscure. This lack of knowledge can be addressed using molecular tools that discriminate the protein from the homologous, ubiquitous paralog aldolase A. The anti-aldolase C antibodies currently available are polyclonal and not highly specific. We obtained the novel monoclonal antibody 9F against human aldolase C, characterized its isoform specificity and tested its performance. First, we investigated the specificity of 9F for aldolase C. Then, using bioinformatic tools coupled to molecular cloning and chemical synthesis approaches, we produced truncated human aldolase C fragments, and assessed 9F binding to these fragments by western blot and ELISA assays. This strategy revealed that residues 85–102 harbor the epitope-containing region recognized by 9F. The efficiency of 9F was demonstrated also for immunoprecipitation assays. Finally, surface plasmon resonance revealed that the protein has a high affinity toward the epitope-containing peptide. Taken together, our findings show that epitope recognition is sequence-driven and is independent of the three-dimensional structure. In conclusion, given its specific molecular interaction, 9F is a novel and powerful tool to investigate aldolase C’s functions in the brain. PMID:24525694

  1. Phase-space structure of the Buckingham's two-body problem

    NASA Astrophysics Data System (ADS)

    Pricopi, D.; Popescu, E.

    2016-06-01

    In this paper, we study the global flow for the two-body problem associated to the Buckingham potential. For this, using McGehee-type transformations, we write the regularized equations of motion. Then, reducing the 4-dimensional phase space to a 2-dimension one, the global flow in the phase plane is described for all possible values of the parameters of the potential and those of the energy and angular momentum constants. Every phase trajectory is interpreted in terms of physical motion, our problem being depicted both geometrically and physically.

  2. Data-adaptive unfolding of nonergodic spectra: Two-Body Random Ensemble

    NASA Astrophysics Data System (ADS)

    Fossion, R.; Torres Vargas, G.; Velázquez, V.; López Vieyra, J. C.

    2015-01-01

    The statistics of spectral fluctuations is sensitive to the unfolding procedure that separates global from local properties. Previously, we presented a parameter-free and data- adaptive unfolding method that we demonstrated to be highly effective for standard random- matrix ensembles from Random Matrix Theory (RMT). More general ensembles often break the ergodicity property, which leads to ambiguities between individual-spectrum averaged and ensemble-averaged fluctuation measures. Here, we apply our data-adaptive unfolding to a nonergodic Two-Body Random Ensemble (TBRE). In the present approach, both fluctuation measures can be calculated simultaneously within the same unfolding step, and possible arbitrarities introduced by traditional unfolding procedures are avoided.

  3. Construction of Effective Electromagnetic Currents for Two-Body Quasipotential Equations

    SciTech Connect

    Dmitri Krioukov

    1998-09-01

    A systematic algebraic approach for the construction of effective electro-magnetic currents consistent with relativistic two-body quasipotential equations is presented. This approach generalizes the Mandelstam formalism and applies it to a generic quasipotential reduction method. The use of Ward-Takahashi identities for the effective currents guarantees conservation of current matrix elements involving any combination of bound and scattering states. This approach is shown to reproduce previous results for current matrix elements for the particular cases of the Gross and Blankenbecler-Sugar equations. A generic method of truncation of the quasipotential effective current with respect to the number of boson exchanges is introduced.

  4. Two-body potential model based on cosine series expansion for ionic materials

    SciTech Connect

    Oda, Takuji; Weber, William J.; Tanigawa, Hisashi

    2015-09-23

    There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potential model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.

  5. A new set of integrals of motion to propagate the perturbed two-body problem

    NASA Astrophysics Data System (ADS)

    Baù, Giulio; Bombardelli, Claudio; Peláez, Jesús

    2013-05-01

    A formulation of the perturbed two-body problem that relies on a new set of orbital elements is presented. The proposed method represents a generalization of the special perturbation method published by Peláez et al. (Celest Mech Dyn Astron 97(2):131-150, 2007) for the case of a perturbing force that is partially or totally derivable from a potential. We accomplish this result by employing a generalized Sundman time transformation in the framework of the projective decomposition, which is a known approach for transforming the two-body problem into a set of linear and regular differential equations of motion. Numerical tests, carried out with examples extensively used in the literature, show the remarkable improvement of the performance of the new method for different kinds of perturbations and eccentricities. In particular, one notable result is that the quadratic dependence of the position error on the time-like argument exhibited by Peláez's method for near-circular motion under the J2 perturbation is transformed into linear. Moreover, the method reveals to be competitive with two very popular element methods derived from the Kustaanheimo-Stiefel and Sperling-Burdet regularizations.

  6. Non-singular orbital elements for special perturbations in the two-body problem

    NASA Astrophysics Data System (ADS)

    Baù, Giulio; Bombardelli, Claudio; Peláez, Jesús; Lorenzini, Enrico

    2015-12-01

    Seven spatial elements and a time element are proposed as the state variables of a new special perturbation method for the two-body problem. The new elements hold for zero eccentricity and inclination and for negative values of the total energy. They are developed by combining a spatial transformation into projective coordinates (as in the Burdet-Ferrándiz regularization) with a time transformation in which the exponent of the orbital radius is equal to one instead of two (as commonly done in the literature). By following this approach, we discover a new linearization of the two-body problem, from which the orbital elements can be generated by the variation of parameters method. The geometrical significance of the spatial quantities is revealed by a new intermediate frame which differs from a local vertical local horizontal frame by one rotation in the instantaneous orbital plane. Four elements parametrize the attitude in space of this frame, which in turn defines the orientation of the orbital plane and fixes the departure direction for the longitude of the propagated body. The remaining three elements determine the motion along the radial unit vector and the orbital longitude. The performance of the method, tested using a series of benchmark orbit propagation scenarios, is extremely good when compared to several regularized formulations, some of which have been modified and improved here for the first time.

  7. Two-body potential model based on cosine series expansion for ionic materials

    DOE PAGESBeta

    Oda, Takuji; Weber, William J.; Tanigawa, Hisashi

    2015-09-23

    There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potentialmore » model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.« less

  8. Applications of the Kustaanheimo-Stieffel transformation of the perturbed two-body problem

    NASA Technical Reports Server (NTRS)

    Bond, V. R.

    1973-01-01

    The Newtonian differential equations of motion for the two-body problem can be transformed into four linear harmonic-oscillator equations by simultaneously applying the regularization step dt/ds = r and the Kustaanheimo-Stieffel (KS) transformation. The regularization step changes the independent variable from time to a new variable s, and the KS transformation transforms the position and velocity vectors from Cartesian space into a four-dimensional space. A derivation of a uniform, regular solution for the perturbed two-body problem in the four-dimensional space is presented. The variation-of-parameters technique is used to develop expressions for the derivatives of ten elements (which are constants in the unperturbed motion) for the general case that includes both perturbations which can arise from a potential and perturbations which cannot be derived from a potential. This ten-element solution has mixed secular terms that degrade the long-term accuracy during numerical integration. Therefore, to eliminate these terms, the solution is modified by introducing two additional elements.

  9. C P -violating polarization asymmetry in charmless two-body decays of beauty baryons

    NASA Astrophysics Data System (ADS)

    He, Min; He, Xiao-Gang; Li, Guan-Nan

    2015-08-01

    Several baryons containing a heavy b-quark, the b-baryons, have been discovered. The charmless two-body decays of b-baryons can provide a new platform for C P violating studies in a similar way provided by charmless two-body decays of B-meson. There are new C P violating observables related to baryon polarization in b-baryon decays. We show that in the flavor S U (3 ) limit, there exists relations involving different combinations of the decay amplitudes compared with those in C P violating rate asymmetry. These new relations therefore provide interesting tests for the mechanism of C P violations in the standard model (SM) and flavor S U (3 ) symmetry. Such tests could complement the b-meson decay studies which hint at a better flavor S U (3 ) conservation in b-hadron decays than in kaon and hyperon decays. Future data from LHCb can provide new information about C P violation in the SM.

  10. The importance of residues 195-206 of human blood clotting factor VII in the interaction of factor VII with tissue factor

    SciTech Connect

    Wildgoose, P.; Kisiel, W.; Kazim, A.L. )

    1990-09-01

    Previous studies indicated that human and bovine factor VII exhibit 71% amino acid sequence identity. In the present study, competition binding experiments revealed that the interaction of human factor VII with cell-surface human tissue factor was not inhibited by 100-fold molar excess of bovine factor VII. This finding indicated that bovine and human factor VII are not structurally homologous in the region(s) where human factor VII interacts with human tissue factor. On this premise, the authors synthesized three peptides corresponding to regions of human factor VII that exhibited marked structural dissimilarity to bovine factor VII; these regions of dissimilarity included residues 195-206, 263-274, and 314-326. Peptide 195-206 inhibited the interaction of factor VII with cell-surface tissue factor and the activation of factor X by a complex of factor VIIa and tissue factor half-maximally at concentrations of 1-2 mM. A structurally rearranged form of peptide 195-206 containing an aspartimide residue inhibited these reactions half-maximally at concentrations of 250-300 {mu}M. In contrast, neither peptide 263-274 nor peptide 314-326, at 2 mM concentration, significantly affected either factor VIIa interaction with tissue factor or factor VIIa-mediated activation of factor X. The data provide presumptive evidence that residues 195-206 of human factor VII are involved in the interaction of human factor VII with the extracellular domain of human tissue factor apoprotein.

  11. Baseline Residual Kidney Function and Its Ensuing Rate of Decline Interact to Predict Mortality of Peritoneal Dialysis Patients

    PubMed Central

    Pérez Fontán, Miguel; Remón Rodríguez, César; da Cunha Naveira, Marta; Borràs Sans, Mercè; Rodríguez Suárez, Carmen; Quirós Ganga, Pedro; Sánchez Alvarez, Emilio; Rodríguez-Carmona, Ana

    2016-01-01

    Background Baseline residual kidney function (RKF) and its rate of decline during follow-up are purported to be reliable outcome predictors of patients undergoing Peritoneal Dialysis (PD). The independent contribution of each of these factors has not been elucidated. Method We report a multicenter, longitudinal study of 493 patients incident on PD and satisfying two conditions: a glomerular filtration rate (GFR) ≥1 mL/minute and a daily diuresis ≥300 mL. The main variables were the GFR (mean of urea and creatinine clearances) at PD inception and the GFR rate of decline during follow-up. The main outcome variable was patient mortality. The secondary outcome variables were: PD technique failure and risk of peritoneal infection. The statistical analysis was based on a multivariate approach, placing an emphasis on the interactions between the two main study variables. Main Results Baseline GFR and its rate of decline performed well as independent predictors of both patient mortality and risk of peritoneal infection. These two main study variables maintained a moderate correlation with each other (r2 = 0.12, p<0.0005), and interacted clearly, as predictors of patient mortality. A low baseline GFR followed by a fast decline portended the worst survival outcome (adjusted HR 3.84, 95%CI 1.81–8.14, p<0.0005)(Ref. baseline GFR above median plus rate of decline below median). In general, the rate of decline of RKF had a greater effect on mortality than baseline GFR, which had no detectable effect on survival when the decline of RKF was slow (HR 1.17, 95% CI 0.81–2.22, p = 0.22). Conversely, a relatively high GFR at the start of PD still carried a significant risk of mortality, when RKF declined rapidly (HR 1.89, 95% CI 1.05–3.72, p = 0.028). Conclusion The risk-benefit balance of an early versus late start of PD cannot be evaluated without taking into consideration the rate of decline of RKF. This circumstance may contribute to explain the controversial results

  12. Geography of the rotational resonances and their stability in the ellipsoidal full two body problem

    NASA Astrophysics Data System (ADS)

    Jafari Nadoushan, Mahdi; Assadian, Nima

    2016-02-01

    A fourth-order Hamiltonian describing the planar full two body problem is obtained, allowing for a mapping out of the geography of spin-spin-orbit resonances. The expansion of the mutual potential function up to the fourth-order results in the angles to come through one single harmonic and consequently the rotation of both bodies and mutual orbit are coupled. Having derived relative equilibria, stability analysis showed that the stability conditions are independent of physical and orbital characteristics. Simultaneously chaotic motion of bodies is investigated through the Chirikov diffusion utilizing geographic information of the complete resonances. The results show that simultaneous chaos among the binary asteroids is not expected to be prevalent due to the mass distribution of primary in compare with secondary. If mass distribution of bodies is of the same order, simultaneous chaos and global instability are achievable.

  13. First results with charmless two-body B-decays at LHCb, and future prospects

    ScienceCinema

    None

    2011-04-25

    LHCb is an experiment which is designed to perform flavour physics measurements at the LHC. Charged two-body charmless B decays (e.g. B^0 -> Kpi, pipi, B_s->KK, etc) receive significant contributions from loop diagrams and are thus sensitive probes of New Physics. Study of these modes is therefore an important physics goal of LHCb. First results will be presented, using around 37 pb^{-1} of data collected at \\sqrt{s}=7 TeV in 2010. These results illustrate the power of the LHCb trigger system and particle identification capabilities of the RICH detectors in isolating clean samples of each final state, and include preliminary measurements of direct CP-violation in certain key modes. The prospects for these measurements in the coming run will be presented. A brief survey will also be given of results and prospect in other areas of the LHCb physics programme.

  14. First results with charmless two-body B-decays at LHCb, and future prospects

    SciTech Connect

    2011-02-22

    LHCb is an experiment which is designed to perform flavour physics measurements at the LHC. Charged two-body charmless B decays (e.g. B^0 -> Kpi, pipi, B_s->KK, etc) receive significant contributions from loop diagrams and are thus sensitive probes of New Physics. Study of these modes is therefore an important physics goal of LHCb. First results will be presented, using around 37 pb^{-1} of data collected at \\sqrt{s}=7 TeV in 2010. These results illustrate the power of the LHCb trigger system and particle identification capabilities of the RICH detectors in isolating clean samples of each final state, and include preliminary measurements of direct CP-violation in certain key modes. The prospects for these measurements in the coming run will be presented. A brief survey will also be given of results and prospect in other areas of the LHCb physics programme.

  15. Opposite charged two-body system of identical counterrotating black holes

    NASA Astrophysics Data System (ADS)

    Cabrera-Munguia, I.; Lämmerzahl, Claus; López, L. A.; Macías, Alfredo

    2013-10-01

    A four-parametric exact solution describing a two-body system of identical Kerr-Newman counterrotating black holes endowed with opposite electric/magnetic charges is presented. The axis conditions are solved in order to really describe two black holes separated by a massless strut. Moreover, the explicit form of the horizon half length parameter σ in terms of physical Komar parameters, i.e., Komar’s mass M, electric charge QE, angular momentum J, and a coordinate distance R is derived. Additionally, magnetic charges QB arise from the rotation of electrically charged black holes. As a consequence, in order to account for the contribution to the mass of the magnetic charge, the usual Smarr mass formula should be generalized, as it is proposed by A. Tomimatsu, Prog. Theor. Phys. 72, 73 (1984).

  16. Numerical integration of a relativistic two-body problem via a multiple scales method

    NASA Astrophysics Data System (ADS)

    Abouelmagd, Elbaz I.; Elshaboury, S. M.; Selim, H. H.

    2016-01-01

    We offer an analytical study on the dynamics of a two-body problem perturbed by small post-Newtonian relativistic term. We prove that, while the angular momentum is not conserved, the motion is planar. We also show that the energy is subject to small changes due to the relativistic effect. We also offer a periodic solution to this problem, obtained by a method based on the separation of time scales. We demonstrate that our solution is more general than the method developed in the book by Brumberg (Essential Relativistic Celestial Mechanics, Hilger, Bristol, 1991). The practical applicability of this model may be in studies of the long-term evolution of relativistic binaries (neutron stars or black holes).

  17. Proton-Nucleus Elastic Cross Sections Using Two-Body In-Medium Scattering Amplitudes

    NASA Technical Reports Server (NTRS)

    Tripathi, R. K.; Wilson, John W.; Cucinotta, Francis A.

    2001-01-01

    Recently, a method was developed of extracting nucleon-nucleon (NN) cross sections in the medium directly from experiment. The in-medium NN cross sections form the basic ingredients of several heavy-ion scattering approaches including the coupled-channel approach developed at the Langley Research Center. The ratio of the real to the imaginary part of the two-body scattering amplitude in the medium was investigated. These ratios are used in combination with the in-medium NN cross sections to calculate elastic proton-nucleus cross sections. The agreement is excellent with the available experimental data. These cross sections are needed for the radiation risk assessment of space missions.

  18. Treatment of the two-body Coulomb problem as a short-range potential

    NASA Astrophysics Data System (ADS)

    Gasaneo, G.; Ancarani, L. U.

    2009-12-01

    The scattering wave function and the transition amplitude for the two-body Coulomb problem are written as power series of the Sommerfeld parameter. Making use of a mathematical study of the nth derivatives of Kummer function with respect to its first parameter, the series coefficients are expressed analytically in terms of multivariable hypergeometric functions. We establish the connection with the Born series based on the free particle Green’s function and show its applicability to long-range potentials. We also relate our analysis to recent works on the distorted-wave theory for the Coulomb problem. For the transition amplitude, the Born series is presented and compared to the series obtained from the exact well-known Rutherford result. Since the two series differ, care must be taken when extracting the relevant information about the scattering. Finally, implications for three-body problems are discussed.

  19. Parametric study of two-body floating-point wave absorber

    NASA Astrophysics Data System (ADS)

    Amiri, Atena; Panahi, Roozbeh; Radfar, Soheil

    2016-03-01

    In this paper, we present a comprehensive numerical simulation of a point wave absorber in deep water. Analyses are performed in both the frequency and time domains. The converter is a two-body floating-point absorber (FPA) with one degree of freedom in the heave direction. Its two parts are connected by a linear mass-spring-damper system. The commercial ANSYS-AQWA software used in this study performs well in considering validations. The velocity potential is obtained by assuming incompressible and irrotational flow. As such, we investigated the effects of wave characteristics on energy conversion and device efficiency, including wave height and wave period, as well as the device diameter, draft, geometry, and damping coefficient. To validate the model, we compared our numerical results with those from similar experiments. Our study results can clearly help to maximize the converter's efficiency when considering specific conditions.

  20. Dark energy in the two-body problem: The local group of galaxies

    NASA Astrophysics Data System (ADS)

    Emelyanov, N. V.; Kovalyov, M. Yu.; Chernin, A. D.

    2015-06-01

    The two-body problem of classical mechanics can be extended in a natural way by introducing a universal dark-energy background, which acts as a third dynamical factor. For real systems of galaxies, the corresponding additional acceleration is described by general relativity in the Newtonian limit, in which deviations from the Minkowski metric are very small. It is shown that this acceleration has the same form in different inertial and non-inertial reference frames. The invariance of the acceleration produced by dark energy reflects the fact that, according to its mechanical properties, dark energy is a vacuum that is comoving with any motion. In this generalized formulation, as in the classical case, the two-body problem with a dark-energy background reduces to the motion of a single body in a central field. Two problems of this kind are considered for the Local Group of galaxies. The first, "internal," problem concerns the binary system formed by the main bodies of the Local Group: our galaxy and M31. The subject of the second, "external," problem is the binary system formed by the Local Group as a whole and its closest neighbor, the Virgo Cluster. In the internal problem, the effect of the dark energy is that the binary system is not bound if its mass does not exceed 3 × 1012 M⊙, which is allowed by the observational data. The external problem demonstrates the possibility of an evolutionary scenario in which a group could initially be located in the volume of a cluster, but then leave it and, moving away with an acceleration created by dark energy, arrive at the observed distance from the cluster.

  1. Energy spectra of massive two-body decay products and mass measurement

    NASA Astrophysics Data System (ADS)

    Agashe, Kaustubh; Franceschini, Roberto; Hong, Sungwoo; Kim, Doojin

    2016-04-01

    We have recently established a new method for measuring the mass of unstable particles produced at hadron colliders based on the analysis of the energy distribution of a mass less product from their two-body decays. The central ingredient of our proposal is the remarkable result that, for an unpolarized decaying particle, the location of the peak in the energy distribution of the observed decay product is identical to the (fixed) value of the energy that this particle would have in the rest-frame of the decaying particle, which, in turn, is a simple function of the involved masses. In addition, we utilized the property that this energy distribution is symmetric around the location of peak when energy is plotted on a logarithmic scale. The general strategy was demonstrated in several specific cases, including both beyond the standard model particles, as well as for the top quark. In the present work, we generalize this method to the case of a massive decay product from a two-body decay; this procedure is far from trivial because (in general) both the above-mentioned properties are no longer valid. Nonetheless, we propose a suitably modified parametrization of the energy distribution that was used successfully for the massless case, which can deal with the massive case as well. We test this parametrization on concrete examples of energy spectra of Z bosons from the decay of a heavier supersymmetric partner of top quark (stop) into a Z boson and a lighter stop. After establishing the accuracy of this parametrization, we study a realistic application for the same process, but now including dominant backgrounds and using foreseeable statistics at LHC14, in order to determine the performance of this method for an actual mass measurement. The upshot of our present and previous work is that, in spite of energy being a Lorentz-variant quantity, its distribution emerges as a powerful tool for mass measurement at hadron colliders.

  2. Elicitin-Induced Distal Systemic Resistance in Plants is Mediated Through the Protein-Protein Interactions Influenced by Selected Lysine Residues.

    PubMed

    Uhlíková, Hana; Obořil, Michal; Klempová, Jitka; Šedo, Ondrej; Zdráhal, Zbyněk; Kašparovský, Tomáš; Skládal, Petr; Lochman, Jan

    2016-01-01

    Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6-7 lysine residues) are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the α-isoforms (with only 1-3 lysine residues). To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of β-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein's charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins' movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance. PMID:26904041

  3. Elicitin-Induced Distal Systemic Resistance in Plants is Mediated Through the Protein–Protein Interactions Influenced by Selected Lysine Residues

    PubMed Central

    Uhlíková, Hana; Obořil, Michal; Klempová, Jitka; Šedo, Ondrej; Zdráhal, Zbyněk; Kašparovský, Tomáš; Skládal, Petr; Lochman, Jan

    2016-01-01

    Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6–7 lysine residues) are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the α-isoforms (with only 1–3 lysine residues). To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of β-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein’s charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins’ movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance. PMID:26904041

  4. Water-soluble LYNX1 Residues Important for Interaction with Muscle-type and/or Neuronal Nicotinic Receptors*

    PubMed Central

    Lyukmanova, Ekaterina N.; Shulepko, Mikhail A.; Buldakova, Svetlana L.; Kasheverov, Igor E.; Shenkarev, Zakhar O.; Reshetnikov, Roman V.; Filkin, Sergey Y.; Kudryavtsev, Denis S.; Ojomoko, Lucy O.; Kryukova, Elena V.; Dolgikh, Dmitry A.; Kirpichnikov, Mikhail P.; Bregestovski, Piotr D.; Tsetlin, Victor I.

    2013-01-01

    Human LYNX1, belonging to the Ly6/neurotoxin family of three-finger proteins, is membrane-tethered with a glycosylphosphatidylinositol anchor and modulates the activity of nicotinic acetylcholine receptors (nAChR). Recent preparation of LYNX1 as an individual protein in the form of water-soluble domain lacking glycosylphosphatidylinositol anchor (ws-LYNX1; Lyukmanova, E. N., Shenkarev, Z. O., Shulepko, M. A., Mineev, K. S., D'Hoedt, D., Kasheverov, I. E., Filkin, S. Y., Krivolapova, A. P., Janickova, H., Dolezal, V., Dolgikh, D. A., Arseniev, A. S., Bertrand, D., Tsetlin, V. I., and Kirpichnikov, M. P. (2011) NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. J. Biol. Chem. 286, 10618–10627) revealed the attachment at the agonist-binding site in the acetylcholine-binding protein (AChBP) and muscle nAChR but outside it, in the neuronal nAChRs. Here, we obtained a series of ws-LYNX1 mutants (T35A, P36A, T37A, R38A, K40A, Y54A, Y57A, K59A) and examined by radioligand analysis or patch clamp technique their interaction with the AChBP, Torpedo californica nAChR and chimeric receptor composed of the α7 nAChR extracellular ligand-binding domain and the transmembrane domain of α1 glycine receptor (α7-GlyR). Against AChBP, there was either no change in activity (T35A, T37A), slight decrease (K40A, K59A), and even enhancement for the rest mutants (most pronounced for P36A and R38A). With both receptors, many mutants lost inhibitory activity, but the increased inhibition was observed for P36A at α7-GlyR. Thus, there are subtype-specific and common ws-LYNX1 residues recognizing distinct targets. Because ws-LYNX1 was inactive against glycine receptor, its “non-classical” binding sites on α7 nAChR should be within the extracellular domain. Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for α-bungarotoxin and

  5. The second-sphere residue T263 is important for the function and catalytic activity of PTP1B via interaction with the WPD-loop.

    PubMed

    Xiao, Peng; Wang, Xiao; Wang, Hong-Mei; Fu, Xiao-Lei; Cui, Fu-ai; Yu, Xiao; Wen, Shi-shuai; Bi, Wen-Xiang; Sun, Jin-Peng

    2014-12-01

    Protein tyrosine phosphatases have diverse substrate specificities and intrinsic activities that lay the foundations for the fine-tuning of a phosphorylation network to precisely regulate cellular signal transduction. All classical PTPs share common catalytic mechanisms, and the important catalytic residues in the first sphere of their active sites have been well characterized. However, little attention has been paid to the second-sphere residues that are potentially important in defining the intrinsic activity and substrate specificity of PTPs. Here, we find that a conserved second-sphere residue, Thr263, located in the surface Q-loop is important for both the function and activity of PTPs. Using PTP1B as a study model, we found that mutations of Thr263 impaired the negative regulation role of PTP1B in insulin signaling. A detailed mechanistic study utilizing steady-state kinetics, Brønsted analysis and pH dependence in the presence of pNPP or phosphopeptide substrates revealed that Thr263 is required for the stabilization of the leaving group during catalysis. Further crystallographic studies and structural comparison revealed that Thr263 regulates the general acid function through modulation of the WPD-loop by the T263:F182/Y/H interaction pair, which is conserved in 26 out of 32 classical PTPs. In addition, the hydrophobic interaction between Thr263 and Arg1159 of the insulin receptor contributes to the substrate specificity of PTP1B. Taken together, our findings demonstrate the general role of the second-sphere residue Thr263 in PTP catalysis. Our findings suggest that the second sphere residues of PTP active site may play important roles in PTP-mediated function in both normal and diseased states. PMID:25450460

  6. Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: importance of the interactions between the D residue and integrin.

    PubMed

    Chen, Chiu-Yueh; Shiu, Jia-Hau; Hsieh, Yao-Husn; Liu, Yu-Chen; Chen, Yen-Chin; Chen, Yi-Chun; Jeng, Wen-Yih; Tang, Ming-Jer; Lo, Szecheng J; Chuang, Woei-Jer

    2009-09-01

    Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin-binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a K(I) of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a K(I) of 49 muM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three two-stranded antiparallel beta-sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four-residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R(2) value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 A was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin alphavbeta3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutant-integrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD-containing ligands and integrin are important for their binding. PMID:19280603

  7. Medium modified two-body scattering amplitude from proton-nucleus total cross-sections

    NASA Technical Reports Server (NTRS)

    Tripathi, R. K.; Wilson, J. W.; Cucinotta, F. A.

    2001-01-01

    Recently (R.K. Tripathi, J.W. Wilson, F.A. Cucinotta, Nucl. Instr. and Meth. B 145 (1998) 277; R.K. Tripathi, F.A. Cucinotta, J.W. Wilson, NASA-TP-1998-208438), we have extracted nucleon-nucleon (N-N) cross-sections in the medium directly from experiment. The in-medium N-N cross-sections form the basic ingredients of several heavy-ion scattering approaches including the coupled-channel approach developed at the NASA Langley Research Center. Here, we investigate the ratio of real to imaginary part of the two-body scattering amplitude in the medium. These ratios are used in combination with the in-medium N-N cross-sections to calculate total proton-nucleus cross-sections. The agreement is excellent with the available experimental data. These cross-sections are needed for the radiation risk assessment of space missions. c2001 Elsevier Science B.V. All rights reserved.

  8. Two-body and three-body contacts for identical Bosons near unitarity.

    PubMed

    Smith, D Hudson; Braaten, Eric; Kang, Daekyoung; Platter, Lucas

    2014-03-21

    In a recent experiment with ultracold trapped Rb85 atoms, Makotyn et al. studied a quantum-degenerate Bose gas in the unitary limit where its scattering length is infinitely large. We show that the observed momentum distributions are compatible with a universal relation that expresses the high-momentum tail in terms of the two-body contact C2 and the three-body contact C3. We determine the contact densities for the unitary Bose gas with number density n to be C2 ≈ 20 n(4/3) and C3 ≈ 2n(5/3). We also show that the observed atom loss rate is compatible with that from 3-atom inelastic collisions, which gives a contribution proportional to C3, but the loss rate is not compatible with that from 2-atom inelastic collisions, which gives a contribution proportional to C2. We point out that the contacts C2 and C3 could be measured independently by using the virial theorem near and at unitarity, respectively. PMID:24702333

  9. The Effective-One-Body Approach to the General Relativistic Two Body Problem

    NASA Astrophysics Data System (ADS)

    Damour, Thibault; Nagar, Alessandro

    The two-body problem in General Relativity has been the subject of many analytical investigations. After reviewing some of the methods used to tackle this problem (and, more generally, the N-body problem), we focus on a new, recently introduced approach to the motion and radiation of (comparable mass) binary systems: the Effective One Body (EOB) formalism. We review the basic elements of this formalism, and discuss some of its recent developments. Several recent comparisons between EOB predictions and Numerical Relativity (NR) simulations have shown the aptitude of the EOB formalism to provide accurate descriptions of the dynamics and radiation of various binary systems (comprising black holes or neutron stars) in regimes that are inaccessible to other analytical approaches (such as the last orbits and the merger of comparable mass black holes). In synergy with NR simulations, post-Newtonian (PN) theory and Gravitational Self-Force (GSF) computations, the EOB formalism is likely to provide an efficient way of computing the very many accurate template waveforms that are needed for Gravitational Wave (GW) data analysis purposes.

  10. Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

    PubMed

    Galindo-Murillo, Rodrigo; Davis, Darrell R; Cheatham, Thomas E

    2016-03-01

    Replication of the HIV-1 virus requires reverse transcription of the viral RNA genome, a process that is specifically initiated by human tRNA3(Lys) packaged within the infectious virion. The primary binding site for the tRNA involves the 3' 18 nucleotides with an additional interaction between an adenine rich loop (A-loop) in the template and the anticodon stem-loop region of the tRNA3(Lys). The loop of the tRNA primer contains two hypermodified base residues and a pseudouridine that are required for a proper binding and activity. Here, we investigate the influence on the structure, dynamics and binding stability of the three modified residues (mnm(5)s(2)U34, t(6)A37 and Ψ39) using extensive molecular dynamics and Quantum Theory of Atoms in Molecules (QTAIM) analysis. Consistent with experiment, the results suggest that the three modified residues are required for faithful binding. Residues mnm(5)s(2)U34 and Ψ39 have a major influence in stabilizing the anticodon loop whereas mnm(5)s(2)U34 and t(6)A37 appear to stabilize the formation of the complex of tRNA3(Lys) with the HIV-1 A-loop. PMID:26655694

  11. On the Accuracy of Sequence-Based Computational Inference of Protein Residues Involved in Interactions with DNA

    PubMed Central

    Gou, Zhenkun; Kuznetsov, Igor B.

    2009-01-01

    Methods for computational inference of DNA-binding residues in DNA-binding proteins are usually developed using classification techniques trained to distinguish between binding and non-binding residues on the basis of known examples observed in experimentally determined high-resolution structures of protein-DNA complexes. What degree of accuracy can be expected when a computational methods is applied to a particular novel protein remains largely unknown. We test the utility of classification methods on the example of Kernel Logistic Regression (KLR) predictors of DNA-binding residues. We show that predictors that utilize sequence properties of proteins can successfully predict DNA-binding residues in proteins from a novel structural class. We use Multiple Linear Regression (MLR) to establish a quantitative relationship between protein properties and the expected accuracy of KLR predictors. Present results indicate that in the case of novel proteins the expected accuracy provided by an MLR model is close to the actual accuracy and can be used to assess the overall confidence of the prediction. PMID:20209034

  12. Complex interactions among residues within pore region determine the K+ dependence of a KAT1-type potassium channel AmKAT1.

    PubMed

    Yang, Guangzhe; Sentenac, Hervé; Véry, Anne-Aliénor; Su, Yanhua

    2015-08-01

    KAT1-type channels mediate K(+) influx into guard cells that enables stomatal opening. In this study, a KAT1-type channel AmKAT1 was cloned from the xerophyte Ammopiptanthus mongolicus. In contrast to most KAT1-type channels, its activation is strongly dependent on external K(+) concentration, so it can be used as a model to explore the mechanism for the K(+) -dependent gating of KAT1-type channels. Domain swapping between AmKAT1 and KAT1 reveals that the S5-pore-S6 region controls the K(+) dependence of AmKAT1, and residue substitutions show that multiple residues within the S5-Pore linker and Pore are involved in its K(+) -dependent gating. Importantly, complex interactions occur among these residues, and it is these interactions that determine its K(+) dependence. Finally, we analyzed the potential mechanism for the K(+) dependence of AmKAT1, which could originate from the requirement of K(+) occupancy in the selectivity filter to maintain its conductive conformation. These results provide new insights into the molecular basis of the K(+) -dependent gating of KAT1-type channels. PMID:26032087

  13. Role of Acidic Residues in Helices TH8–TH9 in Membrane Interactions of the Diphtheria Toxin T Domain

    PubMed Central

    Ghatak, Chiranjib; Rodnin, Mykola V.; Vargas-Uribe, Mauricio; McCluskey, Andrew J.; Flores-Canales, Jose C.; Kurnikova, Maria; Ladokhin, Alexey S.

    2015-01-01

    The pH-triggered membrane insertion of the diphtheria toxin translocation domain (T domain) results in transferring the catalytic domain into the cytosol, which is relevant to potential biomedical applications as a cargo-delivery system. Protonation of residues is suggested to play a key role in the process, and residues E349, D352 and E362 are of particular interest because of their location within the membrane insertion unit TH8–TH9. We have used various spectroscopic, computational and functional assays to characterize the properties of the T domain carrying the double mutation E349Q/D352N or the single mutation E362Q. Vesicle leakage measurements indicate that both mutants interact with the membrane under less acidic conditions than the wild-type. Thermal unfolding and fluorescence measurements, complemented with molecular dynamics simulations, suggest that the mutant E362Q is more susceptible to acid destabilization because of disruption of native intramolecular contacts. Fluorescence experiments show that removal of the charge in E362Q, and not in E349Q/D352N, is important for insertion of TH8–TH9. Both mutants adopt a final functional state upon further acidification. We conclude that these acidic residues are involved in the pH-dependent action of the T domain, and their replacements can be used for fine tuning the pH range of membrane interactions. PMID:25875295

  14. Transmembrane Domain Interactions and Residue Proline 378 Are Essential for Proper Structure, Especially Disulfide Bond Formation, in the Human Vitamin K-Dependent γ-Glutamyl Carboxylase†

    PubMed Central

    Tie, Jian-Ke; Zheng, Mei-Yan; Hsiao, Kuang-Ling N.; Perera, Lalith; Stafford, Darrel W.; Straight, David L.

    2009-01-01

    We used recombinant techniques to create a two-chain form (residues 1–345 and residues 346–758) of the vitamin K-dependent γ-glutamyl carboxylase, a glycoprotein located in the endoplasmic reticulum containing five transmembrane domains. The two-chain carboxylase had carboxylase and epoxidase activities similar to those of one-chain carboxylase. In addition, it had normal affinity for the propeptide of factor IX. We employed this molecule to investigate formation of the one disulfide bond in carboxylase, the transmembrane structure of carboxylase, and the potential interactions among the carboxylase’s transmembrane domains. Our results indicate that the two peptides of the two-chain carboxylase are joined by a disulfide bond. Proline 378 is important for the structure necessary for disulfide formation. Results with the P378L carboxylase indicate that noncovalent bonds maintain the two-chain structure even when the disulfide bond is disrupted. As we had previously proposed, the fifth transmembrane domain of carboxylase is the last and only transmembrane domain in the C-terminal peptide of the two-chain carboxylase. We show that the noncovalent association between the two chains of carboxylase involves an interaction between the fifth transmembrane domain and the second transmembrane domain. Results of a homology model of transmembrane domains 2 and 5 suggest that not only do these two domains associate but that transmembrane domain 2 may interact with another transmembrane domain. This latter interaction may be mediated at least in part by a motif of glycine residues in the second transmembrane domain. PMID:18498174

  15. The interaction between natural organic matter in raw waters and pesticide residues: a three dimensional excitation-emission matrix (3DEEM) fluorescence investigation.

    PubMed

    Beale, David J; Porter, Nichola A; Roddick, Felicity A

    2013-01-01

    This paper examines the interaction between dissolved natural organic matter and pesticide residues, both of which are found in raw water sources, using three dimensional excitation-emission matrix (3DEEM) fluorescence spectroscopy. It was observed that pesticide residue at 0.1 mg L(-1) formed a complex with humic-like fluorophores that are commonly found in raw water samples. Applying 3DEEM fluorescence to investigate the humic fractions, it was found that identification of changes in water sources was possible, and, importantly, the presence of a number of pesticides was able to be determined. In addition, the formation of this complex, and the influence of soluble cations and anions upon it, was shown to impact the efficiency of analytical extraction procedures for pesticides; however, 3DEEM fluorescence could be an approach to account for such losses. PMID:23752373

  16. Residual Symmetry and Explicit Soliton-Cnoidal Wave Interaction Solutions of the (2+1)-Dimensional KdV-mKdV Equation

    NASA Astrophysics Data System (ADS)

    Cheng, Wenguang; Li, Biao

    2016-04-01

    The truncated Painlevé method is developed to obtain the nonlocal residual symmetry and the Bäcklund transformation for the (2+1)-dimensional KdV-mKdV equation. The residual symmetry is localised after embedding the (2+1)-dimensional KdV-mKdV equation to an enlarged one. The symmetry group transformation of the enlarged system is computed. Furthermore, the (2+1)-dimensional KdV-mKdV equation is proved to be consistent Riccati expansion (CRE) solvable. The soliton-cnoidal wave interaction solution in terms of the Jacobi elliptic functions and the third type of incomplete elliptic integral is obtained by using the consistent tanh expansion (CTE) method, which is a special form of CRE.

  17. The role of N-terminal and C-terminal Arg residues from BK on interaction with kinin B2 receptor.

    PubMed

    Filippelli-Silva, Rafael; Martin, Renan P; Rodrigues, Eliete S; Nakaie, Clovis R; Oliveira, Laerte; Pesquero, João B; Shimuta, Suma I

    2016-04-01

    Bradykinin (BK) is a nonapeptide important for several physiological processes such as vasodilatation, increase in vascular permeability and release of inflammatory mediators. BK performs its actions by coupling to and activating the B2 receptor, a family A G-protein coupled receptor. Using a strategy which allows systematical monitoring of BK R1 and R9 residues and B2 receptor acidic residues Glu5.35(226) and Asp6.58(298), our study aims at clarifying the BK interaction profile with the B2 receptor [receptor residue numbers are normalized according to Ballesteros and Weinstein, Methods Neurosci. 25 (1995), pp. 366-428) followed by receptor sequence numbering in brackets]. N- and C-terminal analogs of BK (-A1, -G1, -K1, -E1 and BK-A9) were tested against wild type B2, Glu5.35(226)Ala and Asp6.58(298)Ala B2 mutant receptors for their affinity and capability to elicit responses by mechanical recordings of isolated mice stomach fundus, measuring intracellular calcium mobilization, and competitive fluorimetric binding assays. BK showed 2- and 15-fold decreased potency for Glu5.35(226) and Asp6.58(298) B2 mutant receptors, respectively. In B2-Glu5.35(226)Ala BK analogs showed milder reduction in evaluated parameters. On the other hand, in the B2-Asp6.58(298)Ala mutant, no N-terminal analog was able to elicit any response. However, the BK-A9 analog presented higher affinity parameters than BK in the latter mutant. These findings provide enough support for defining a novel interaction role of BK-R9 and Asp6.58(298) receptor residues. PMID:26584354

  18. Modified Kepler's law, escape speed, and two-body problem in modified Newtonian dynamics-like theories

    NASA Astrophysics Data System (ADS)

    Zhao, Hongsheng; Li, Baojiu; Bienaymé, Olivier

    2010-11-01

    We derive a simple analytical expression for the two-body force in a subclass of modified Newtonian dynamics (MOND) theories and make testable predictions in the modification to the two-body orbital period, shape, precession rate, escape speed, etc. We demonstrate the applications of the modified Kepler’s law in the timing of satellite orbits around the Milky Way, and checking the feasibility of MOND in the orbit of the large Magellanic cloud, the M31 galaxy, and the merging bullet clusters. MOND appears to be consistent with satellite orbits although with a tight margin. Our results on two-bodies are also generalized to restricted three-body, many-body problems, rings, and shells.

  19. Quantum oscillation signatures of spin-orbit interactions controlling the residual nodal bilayer-splitting in underdoped high-Tc cuprates

    NASA Astrophysics Data System (ADS)

    Harrison, Neil; Shekhter, Arkady

    2015-03-01

    We investigate the origin of the small residual nodal bilayer-splitting in the underdoped high-Tc superconductor YBa2Cu3O6+x using the results of recently published angle-resolved quantum oscillation data [Sebastian et al., Nature 511, 61 (2014)]. A crucial clue to the origin of the residual bilayer-splitting is found to be provided by the anomalously small Zeeman-splitting of some of the observed cyclotron orbits. We show that such an anomalously Zeeman-splitting (or small effective g-factor) for a subset of orbits can be explained by spin-orbit interactions, which become significant in the nodal regions as a result of the vanishing bilayer coupling. The primary effect of spin-orbit interactions is to cause quasiparticles traversing the nodal region of the Brillouin zone to undergo a spin flip. We suggest that the Rashba-like spin-orbit interactions, naturally present in bilayer systems, have the right symmetry and magnitude to give rise to a network of coupled orbits consistent with experimental observations in underdoped YBa2Cu3O6+x. This work is supported by the DOEm BES proposal LANLF100, while the magnet lab is supported by the NSF and Florida State.

  20. Hydrophilic Residues Are Crucial for Ribosomal Protein L11 (RPL11) Interaction with Zinc Finger Domain of MDM2 and p53 Protein Activation*

    PubMed Central

    Zhang, Qi; Xiao, Hui; Chai, Sergio C.; Hoang, Quyen Q.; Lu, Hua

    2011-01-01

    Ribosomal protein L11 (RPL11) has been shown to activate p53 by binding to MDM2 and negating its p53 suppression activity in response to ribosomal stress. Although a mutation at Cys-305 within the zinc finger domain of MDM2 has been shown to drastically impair MDM2 interaction with RPL11 and thus escapes the inhibition by this ribosomal protein, it still remains elusive whether RPL11 inactivates MDM2 via direct action on this zinc finger domain and what is the chemical nature of this specific interaction. To define the roles of the MDM2 zinc finger in association with RPL11, we conducted hydrogen-deuterium exchange mass spectrometry, computational modeling, circular dichroism, and mutational analyses of the zinc finger domain of MDM2 and human RPL11. Our study reveals that RPL11 forms a stable complex with MDM2 in vitro through direct contact with its zinc finger. This binding is disrupted by single mutations of non-cysteine amino acids within the zinc finger domain of MDM2. Basic residues in RPL11 are crucial for the stable binding and RPL11 suppression of MDM2 activity toward p53. These results provide the first line of evidence for the specific interaction between RPL11 and the zinc finger of MDM2 via hydrophilic residues as well as a molecular foundation for better understanding RPL11 inhibition of MDM2 function. PMID:21903592

  1. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein-Protein Interactions.

    PubMed

    Gutierrez, Craig B; Yu, Clinton; Novitsky, Eric J; Huszagh, Alexander S; Rychnovsky, Scott D; Huang, Lan

    2016-08-16

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein-protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MS(n)). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MS(n). Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  2. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein–Protein Interactions

    PubMed Central

    2016-01-01

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein–protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MSn). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MSn. Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  3. Identification of Conserved Amino Acid Residues of the Salmonella σS Chaperone Crl Involved in Crl-σS Interactions

    PubMed Central

    Monteil, Véronique; Kolb, Annie; D'Alayer, Jacques; Beguin, Pierre; Norel, Françoise

    2010-01-01

    Proteins that bind σ factors typically attenuate the function of the σ factor by restricting its access to the RNA polymerase (RNAP) core enzyme. An exception to this general rule is the Crl protein that binds the stationary-phase sigma factor σS (RpoS) and enhances its affinity for the RNAP core enzyme, thereby increasing expression of σS-dependent genes. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than rpoS. Seventeen residues are conserved in all members of the Crl family. Site-directed mutagenesis of the crl gene from Salmonella enterica serovar Typhimurium and complementation of a Δcrl mutant of Salmonella indicated that substitution of the conserved residues Y22, F53, W56, and W82 decreased Crl activity. This conclusion was further confirmed by promoter binding and abortive transcription assays. We also used a bacterial two-hybrid system (BACTH) to show that the four substitutions in Crl abolish Crl-σS interaction and that residues 1 to 71 in σS are dispensable for Crl binding. In Escherichia coli, it has been reported that Crl also interacts with the ferric uptake regulator Fur and that Fur represses crl transcription. However, the Salmonella Crl and Fur proteins did not interact in the BACTH system. In addition, a fur mutation did not have any significant effect on the expression level of Crl in Salmonella. These results suggest that the relationship between Crl and Fur is different in Salmonella and E. coli. PMID:20008066

  4. The full two-body-problem: Simulation, analysis, and application to the dynamics, characteristics, and evolution of binary asteroid systems

    NASA Astrophysics Data System (ADS)

    Fahnestock, Eugene Gregory

    The Full Two-Body-Problem (F2BP) describes the dynamics of two unconstrained rigid bodies in close proximity, having arbitrary spatial distribution of mass, charge, or similar field quantity, and interacting through a mutual potential dependent on that distribution. While the F2BP has applications in areas as wide ranging as molecular dynamics to satellite formation flying, this dissertation focuses on its application to natural bodies in space with nontrivial mass distribution interacting through mutual gravitational potential, i.e. binary asteroids. This dissertation first describes further development and implementation of methods for accurate and efficient F2BP propagation based upon a flexible method for computing the mutual potential between bodies modeled as homogenous polyhedra. Next application of these numerical tools to the study of binary asteroid (66391) 1999 KW4 is summarized. This system typifies the largest class of NEO binaries, which includes nearly half of them, characterized by a roughly oblate spheroid primary rotating rapidly and roughly triaxial ellipsoid secondary in on-average synchronous rotation. Thus KW4's dynamics generalize to any member of that class. Analytical formulae are developed which separately describe the effects of primary oblateness and secondary triaxial ellipsoid shape on frequencies of system motions revealed through the F2BP simulation. These formulae are useful for estimating inertia elements and highest-level internal mass distributions of bodies in any similar system, simply from standoff observation of these motion frequencies. Finally precise dynamical simulation and analysis of the motion of test particles within the time-varying gravity field of the F2BP system is detailed. This Restricted Full-detail Three-Body-Problem encompasses exploration of three types of particle motion within a binary asteroid: (1) Orbital motion such as that for a spacecraft flying within the system about the primary, secondary, or

  5. Proton-hydrogen reaction in an effectively two-body model

    SciTech Connect

    Pupyshev, V. V.

    2013-02-15

    A model of total interaction between a proton incident to a hydrogen atom and the proton that is the nucleus of this atom is proposed. This interaction is assumed to be the sum of the short-range nuclear Reid potential and the long-range Thomas-Fermi potential induced by the Coulomb interaction of the electron with the nucleus of the hydrogen atom. The explicit low-energy asymptotic behavior of the cross section for the proton-hydrogen reaction leading to deuteron production is found. It is shown that this cross section increases in inverse proportion to the collision energy for the proton and hydrogen atom in its zero limit.

  6. Essential role of extracellular charged residues of the human CCK(1) receptor for interactions with SR 146131, SR 27897 and CCK-8S.

    PubMed

    Gouldson, P; Legoux, P; Carillon, C; Dumont, X; Le Fur, G; Ferrara, P; Shire, D

    2000-02-18

    We hypothesized that charge-charge interactions may be important for the binding of the human cholecystokinin type 1 (CCK(1)) receptor-specific non-peptide full agonist SR 146131, (2-[4-(4-chloro-2, 5-dimethoxyphenyl)-5-(2-cyclohexyl-ethyl)-thiazol-2-ylcarbamoyl ]-5, 7-dimethyl-indol-1-yl-1-acetic acid), the competitive antagonist SR 27897, (1-[2-(4-(2-chlorophenyl)thiazol-2-yl) aminocarbonyl indoyl] acetic acid) and the natural octapeptide CCK-8S to the CCK(1) receptor. Alanine replacement studies of positively charged residues in the extracellular domains of the receptor showed that only the R336A mutation affected SR 146131 potency of mutated receptors transiently expressed in monkey kidney epithelial COS-7 cells. Two residues, Lys(115) and Lys(187), were implicated in SR 27897 binding. Only the replacement of Lys(115), Arg(197) and Arg(336) significantly affected CCK-8S binding or activity. These results clearly indicated the importance of certain charged residues, but not others, in SR 146131, SR 27897 and CCK-8S binding. Furthermore, although these molecules probably occupy different binding sites on the CCK(1) receptor, we show that a small non-peptide agonist, SR 146131, can stimulate the dual signaling pathways mediated by the CCK(1) receptor. PMID:10688974

  7. Conserved transmembrane glycine residues in the Shigella flexneri polysaccharide co-polymerase protein WzzB influence protein-protein interactions.

    PubMed

    Papadopoulos, Magdalene; Tran, Elizabeth Ngoc Hoa; Murray, Gerald Laurence; Morona, Renato

    2016-06-01

    The O antigen (Oag) component of lipopolysaccharides (LPS) is crucial for virulence and Oag chain-length regulation is controlled by the polysaccharide co-polymerase class 1 (PCP1) proteins. Crystal structure analyses indicate that structural conservation among PCP1 proteins is highly maintained, however the mechanism of Oag modal-chain-length control remains to be fully elucidated. Shigella flexneri PCP1 protein WzzBSF confers a modal-chain length of 10-17 Oag repeat units (RUs), whereas the Salmonella enterica Typhimurium PCP1 protein WzzBST confers a modal-chain length of ~16-28 Oag RUs. Both proteins share >70 % overall sequence identity and contain two transmembrane (TM1 and TM2) regions, whereby a conserved proline-glycine-rich motif overlapping the TM2 region is identical in both proteins. Conserved glycine residues within TM2 are functionally important, as glycine to alanine substitutions at positions 305 and 311 confer very short Oag modal-chain length (~2-6 Oag RUs). In this study, WzzBSF was co-expressed with WzzBST in S. flexneri and a single intermediate modal-chain length of ~11-21 Oag RUs was observed, suggesting the presence of Wzz:Wzz interactions. Interestingly, co-expression of WzzBSF with WzzBG305A/G311A conferred a bimodal LPS Oag chain length (despite over 99 % protein sequence identity), and we hypothesized that the proteins fail to interact. Co-purification assays detected His6-WzzBSF co-purifying with FLAG-tagged WzzBST but not with FLAG-tagged WzzBG305A/G311A, supporting our hypothesis. These data indicate that the conserved glycine residues in TM2 are involved in Wzz:Wzz interactions, and provide insight into key interactions that drive Oag modal length control. PMID:27028755

  8. Bulged residues promote the progression of a loop–loop interaction to a stable and inhibitory antisense–target RNA complex

    PubMed Central

    Kolb, Fabrice A.; Westhof, Eric; Ehresmann, Chantal; Ehresmann, Bernard; Wagner, E. Gerhart H.; Romby, Pascale

    2001-01-01

    In several groups of bacterial plasmids, antisense RNAs regulate copy number through inhibition of replication initiator protein synthesis. These RNAs are characterized by a long hairpin structure interrupted by several unpaired residues or bulged loops. In plasmid R1, the inhibitory complex between the antisense RNA (CopA) and its target mRNA (CopT) is characterized by a four-way junction structure and a side-by-side helical alignment. This topology facilitates the formation of a stabilizer intermolecular helix between distal regions of both RNAs, essential for in vivo control. The bulged residues in CopA/CopT were shown to be required for high in vitro binding rate and in vivo activity. This study addresses the question of why removal of bulged nucleotides blocks stable complex formation. Structure mapping, modification interference, and molecular modeling of bulged-less mutant CopA–CopT complexes suggests that, subsequent to loop–loop contact, helix propagation is prevented. Instead, a fully base paired loop–loop interaction is formed, inducing a continuous stacking of three helices. Consequently, the stabilizer helix cannot be formed, and stable complex formation is blocked. In contrast to the four-way junction topology, the loop–loop interaction alone failed to prevent ribosome binding at its loading site and, thus, inhibition of RepA translation was alleviated. PMID:11470871

  9. Peptide aromatic interactions modulated by fluorinated residues: Synthesis, structure and biological activity of Somatostatin analogs containing 3-(3′,5′difluorophenyl)-alanine

    PubMed Central

    Martín-Gago, Pablo; Rol, Álvaro; Todorovski, Toni; Aragón, Eric; Martin-Malpartida, Pau; Verdaguer, Xavier; Vallès Miret, Mariona; Fernández-Carneado, Jimena; Ponsati, Berta; Macias, Maria J.; Riera, Antoni

    2016-01-01

    Somatostatin is a 14-residue peptide hormone that regulates the endocrine system by binding to five G-protein-coupled receptors (SSTR1–5). We have designed six new Somatostatin analogs with L-3-(3′,5′-difluorophenyl)-alanine (Dfp) as a substitute of Phe and studied the effect of an electron-poor aromatic ring in the network of aromatic interactions present in Somatostatin. Replacement of each of the Phe residues (positions 6, 7 and 11) by Dfp and use of a D-Trp8 yielded peptides whose main conformations could be characterized in aqueous solution by NMR. Receptor binding studies revealed that the analog with Dfp at position 7 displayed a remarkable affinity to SSTR2 and SSTR3. Analogs with Dfp at positions 6 or 11 displayed a π-π interaction with the Phe present at 11 or 6, respectively. Interestingly, these analogs, particularly [D-Trp8,L-Dfp11]-SRIF, showed high selectivity towards SSTR2, with a higher value than that of Octreotide and a similar one to that of native Somatostatin. PMID:27271737

  10. Peptide aromatic interactions modulated by fluorinated residues: Synthesis, structure and biological activity of Somatostatin analogs containing 3-(3',5'difluorophenyl)-alanine.

    PubMed

    Martín-Gago, Pablo; Rol, Álvaro; Todorovski, Toni; Aragón, Eric; Martin-Malpartida, Pau; Verdaguer, Xavier; Vallès Miret, Mariona; Fernández-Carneado, Jimena; Ponsati, Berta; Macias, Maria J; Riera, Antoni

    2016-01-01

    Somatostatin is a 14-residue peptide hormone that regulates the endocrine system by binding to five G-protein-coupled receptors (SSTR1-5). We have designed six new Somatostatin analogs with L-3-(3',5'-difluorophenyl)-alanine (Dfp) as a substitute of Phe and studied the effect of an electron-poor aromatic ring in the network of aromatic interactions present in Somatostatin. Replacement of each of the Phe residues (positions 6, 7 and 11) by Dfp and use of a D-Trp8 yielded peptides whose main conformations could be characterized in aqueous solution by NMR. Receptor binding studies revealed that the analog with Dfp at position 7 displayed a remarkable affinity to SSTR2 and SSTR3. Analogs with Dfp at positions 6 or 11 displayed a π-π interaction with the Phe present at 11 or 6, respectively. Interestingly, these analogs, particularly [D-Trp8,L-Dfp11]-SRIF, showed high selectivity towards SSTR2, with a higher value than that of Octreotide and a similar one to that of native Somatostatin. PMID:27271737

  11. β- transitions of 16 7N9 → 16 8O8 with optimized SDI residual interaction using pnTDA and TDA approximations

    NASA Astrophysics Data System (ADS)

    Pahlavani, M. R.; Firoozi, B.

    2015-11-01

    Within a developed particle-hole approach, a systematic study of the β- transition from the ground state of the 16N nucleus to the ground and some exited states of the 16O nucleus has been carried out. The energy spectrum and the wave functions of pure configuration of the 16N and 16O nuclei are numerically obtained using the mean-field shell model with respect to the Woods-Saxon nuclear potential accompanying spin-orbit and Coulomb interaction. Considering SDI residual interaction, mixed configuration of ground and excited pnTDA and TDA states are extracted for the aforementioned nucleus. These energy spectra and corresponding eigenstates are highly correspondent to the experimental energy spectrum and eigenstates after adjusting the residual potential parameters using the Nelder-Mead (NM) algorithm. In this approach, the endpoint energy, log ft and the partial half-lives of some possible transitions are calculated. The obtained results using the optimized SDI approach are reasonably close to the available experimental data.

  12. Quasiforbidden two-body Förster resonances in a cold Cs Rydberg gas

    NASA Astrophysics Data System (ADS)

    Pelle, B.; Faoro, R.; Billy, J.; Arimondo, E.; Pillet, P.; Cheinet, P.

    2016-02-01

    Cold Rydberg atoms are known to display dipole-dipole interaction-allowed resonances, also called Förster resonances, which lead to an efficient energy transfer when the proper electric field is used. This electric field also enables resonances, which do not respect the dipole-dipole selection rules under zero field. A few of these quasiforbidden resonances have been observed but they are often overlooked. Here we show that in cold 133Cs atoms there is a large number of these resonances that display a significant transfer efficiency due to their strong interactions, even at low electric field. We also develop a graphical method enabling us to find all possible resonances simultaneously. The resulting dramatic increase in the total number of addressable resonant energy transfers at different electric fields could have implications in the search for few-body interactions or macromolecules built from Rydberg atoms.

  13. Residue Substitutions Near the Redox Center of Bacillus subtilis Spx Affect RNA Polymerase Interaction, Redox Control, and Spx-DNA Contact at a Conserved cis-Acting Element

    PubMed Central

    Lin, Ann A.; Walthers, Don

    2013-01-01

    Spx, a member of the ArsC protein family, is a regulatory factor that interacts with RNA polymerase (RNAP). It is highly conserved in Gram-positive bacteria and controls transcription on a genome-wide scale in response to oxidative stress. The structural requirements for RNAP interaction and promoter DNA recognition by Spx were examined through mutational analysis. Residues near the CxxC redox disulfide center of Spx functioned in RNAP α subunit interaction and in promoter DNA binding. R60E and C10A mutants were shown previously to confer defects in transcriptional activation, but both were able to interact with RNAP. R92, which is conserved in ArsC-family proteins, is likely involved in redox control of Spx, as the C10A mutation, which blocks disulfide formation, was epistatic to the R92A mutation. The R91A mutation reduced transcriptional activation and repression, suggesting a defect in RNAP interaction, which was confirmed by interaction assays using an epitope-tagged mutant protein. Protein-DNA cross-linking detected contact between RNAP-bound Spx and the AGCA element at −44 that is conserved in Spx-controlled genes. This interaction caused repositioning of the RNAP σA subunit from a −35-like element upstream of the trxB (thioredoxin reductase) promoter to positions −36 and −11 of the core promoter. The study shows that RNAP-bound Spx contacts a conserved upstream promoter sequence element when bound to RNAP. PMID:23813734

  14. Adsorption of charged protein residues on an inorganic nanosheet: Computer simulation of LDH interaction with ion channel

    NASA Astrophysics Data System (ADS)

    Tsukanov, Alexey A.; Psakhie, Sergey G.

    2016-08-01

    Quasi-two-dimensional and hybrid nanomaterials based on layered double hydroxides (LDH), cationic clays, layered oxyhydroxides and hydroxides of metals possess large specific surface area and strong electrostatic properties with permanent or pH-dependent electric charge. Such nanomaterials may impact cellular electrostatics, changing the ion balance, pH and membrane potential. Selective ion adsorption/exchange may alter the transmembrane electrochemical gradient, disrupting potential-dependent cellular processes. Cellular proteins as a rule have charged residues which can be effectively adsorbed on the surface of layered hydroxide based nanomaterials. The aim of this study is to attempt to shed some light on the possibility and mechanisms of protein "adhesion" an LDH nanosheet and to propose a new direction in anticancer medicine, based on physical impact and strong electrostatics. An unbiased molecular dynamics simulation was performed and the combined process free energy estimation (COPFEE) approach was used.

  15. Quantum few-body problem with internal structure. I. Two-body problem

    SciTech Connect

    Kuperin, Yu.A.; Makarov, K.A.; Merkur'ev, S.P.; Motovilov, A.K.; Pavlov, B.S.

    1988-12-01

    The methods of the theory of extensions to an auxiliary Hilbert space are used to construct in the two-particle sector a scattering theory for particles possessing internal structure. The analytic properties of the amplitudes of resonance scattering and Green's functions corresponding to a class of singular energy-dependent interactions are investigated.

  16. A Combined Genetic-Proteomic Approach Identifies Residues within Dengue Virus NS4B Critical for Interaction with NS3 and Viral Replication

    PubMed Central

    Chatel-Chaix, Laurent; Fischl, Wolfgang; Scaturro, Pietro; Cortese, Mirko; Kallis, Stephanie; Bartenschlager, Marie; Fischer, Bernd

    2015-01-01

    ABSTRACT Dengue virus (DENV) infection causes the most prevalent arthropod-borne viral disease worldwide. Approved vaccines are not available, and targets suitable for the development of antiviral drugs are lacking. One possible drug target is nonstructural protein 4B (NS4B), because it is absolutely required for virus replication; however, its exact role in the DENV replication cycle is largely unknown. With the aim of mapping NS4B determinants critical for DENV replication, we performed a reverse genetic screening of 33 NS4B mutants in the context of an infectious DENV genome. While the majority of these mutations were lethal, for several of them, we were able to select for second-site pseudoreversions, most often residing in NS4B and restoring replication competence. To identify all viral NS4B interaction partners, we engineered a fully viable DENV genome encoding an affinity-tagged NS4B. Mass spectrometry-based analysis of the NS4B complex isolated from infected cells identified the NS3 protease/helicase as a major interaction partner of NS4B. By combining the genetic complementation map of NS4B with a replication-independent expression system, we identified the NS4B cytosolic loop—more precisely, amino acid residue Q134—as a critical determinant for NS4B-NS3 interaction. An alanine substitution at this site completely abrogated the interaction and DENV RNA replication, and both were restored by pseudoreversions A69S and A137V. This strict correlation between the degree of NS4B-NS3 interaction and DENV replication provides strong evidence that this viral protein complex plays a pivotal role during the DENV replication cycle, hence representing a promising target for novel antiviral strategies. IMPORTANCE With no approved therapy or vaccine against dengue virus infection, the viral nonstructural protein 4B (NS4B) represents a possible drug target, because it is indispensable for virus replication. However, little is known about its precise structure and

  17. 1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residues in complexes of brodimoprim analogues and Lactobacillus casei dihydrofolate reductase.

    PubMed

    Morgan, W D; Birdsall, B; Nieto, P M; Gargaro, A R; Feeney, J

    1999-02-16

    1H and 15N NMR studies have been undertaken on complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with analogues of the antibacterial drug brodimoprim (2,4-diamino-5-(3', 5'-dimethoxy-4'-bromobenzyl)pyrimidine) in order to monitor interactions between carboxylate groups on the ligands and basic residues in the protein. These analogues had been designed by computer modeling with carboxylated alkyl chains introduced at the 3'-O position in order to improve their binding properties by making additional interactions with basic groups in the protein. Specific interactions between ligand carboxylate groups and the conserved Arg57 residue have been detected in studies of 1H/15N HSQC spectra of complexes of DHFR with both the 4-carboxylate and the 4, 6-dicarboxylate brodimoprim analogues. The spectra from both complexes showed four resolved signals for the four NHeta protons of the guanidino group of Arg57, and this is consistent with hindered rotation in the guanidino group resulting from interactions with the 4-carboxylate group in each analogue. In the spectra of each complex, one of the protons from each of the two NH2 groups and both nitrogens are considerably deshielded compared to the shielding values normally observed for such nuclei. This pattern of deshielding is that expected for a symmetrical end-on interaction of the carboxylate oxygens with the NHeta12 and NHeta22 guanidino protons. The differences in the degree of deshielding between the complexes of the two structurally similar brodimoprim analogues and the methotrexate indicates that the shielding is very sensitive to geometry, most probably to hydrogen bond lengths. The 1H/15N HSQC spectrum of the DHFR complex with the brodimoprim-6-carboxylate analogue does not feature any deshielded Arg NHeta protons and this argues against a similar interaction with the Arg57 in this case. It has not proved possible to determine whether the 6-carboxylate in this analogue is interacting directly with

  18. Flavodoxin-mediated electron transfer from photosystem I to ferredoxin-NADP+ reductase in Anabaena: role of flavodoxin hydrophobic residues in protein-protein interactions.

    PubMed

    Goñi, Guillermina; Serrano, Ana; Frago, Susana; Hervás, Manuel; Peregrina, José Ramón; De la Rosa, Miguel A; Gómez-Moreno, Carlos; Navarro, José A; Medina, Milagros

    2008-01-29

    Three surface hydrophobic residues located at the Anabaena flavodoxin (Fld) putative complex interface with its redox partners were replaced by site-directed mutagenesis. The effects of these replacements on Fld interaction with both its physiological electron donor, photosystem I (PSI), and its electron acceptor, ferredoxin-NADP+ reductase (FNR), were analyzed. Trp57, Ile59, and Ile92 contributed to the optimal orientation and tightening of the FNR:Fld and PSI:Fld complexes. However, these side chains did not appear to be involved in crucial specific interactions, but rather contributed to the obtainment of the optimal orientation and distance of the redox centers required for efficient electron transfer. This supports the idea that the interaction of Fld with its partners is less specific than that of ferredoxin and that more than one orientation is efficient for electron transfer in these transient complexes. Additionally, for some of the analyzed processes, WT Fld seems not to be the most optimized molecular species. Therefore, subtle changes at the isoalloxazine environment not only influence the Fld binding abilities, but also modulate the electron exchange processes by producing different orientations and distances between the redox centers. Finally, the weaker apoflavodoxin interaction with FNR suggests that the solvent-accessible region of FMN plays a role either in complex formation with FNR or in providing the adequate conformation of the FNR binding region in Fld. PMID:18177021

  19. The Role of a Second-Shell Residue in Modifying Substrate and Inhibitor Interactions in the SHV β-Lactamase: A Study of Ambler Position Asn276†

    PubMed Central

    Drawz, Sarah M.; Bethel, Christopher R.; Hujer, Kristine M.; Hurless, Kelly N.; Distler, Anne M.; Caselli, Emilia; Prati, Fabio; Bonomo, Robert A.

    2014-01-01

    Inhibitor-resistant class A β-lactamases of the TEM and SHV families that arise by single amino acid substitutions are a significant threat to the efficacy of β-lactam/β-lactamase inhibitor combinations. To better understand the basis of the inhibitor-resistant phenotype in SHV, we performed mutagenesis to examine the role of a second-shell residue, Asn276. Of the 19 variants expressed in Escherichia coli, only the Asn276Asp enzyme demonstrated reduced susceptibility to ampicillin/clavulanate (MIC increased from 50/2 → 50/8 μg/mL) while maintaining high-level resistance to ampicillin (MIC = 8192 μg/mL). Steady-state kinetic analyses of Asn276Asp revealed slightly diminished kcat/Km for all substrates tested. In contrast, we observed a 5-fold increase in Ki for clavulanate (7.4 ± 0.9 μM for Asn276Asp vs 1.4 ± 0.2 μM for SHV-1) and a 40% reduction in kinact/KI (0.013 ± 0.002 μM−1 s−1 for Asn276Asp vs 0.021 ± 0.004 μM−1 s−1 for SHV-1). Timed electrospray ionization mass spectrometry of clavulanate-inhibited SHV-1 and SHV Asn276Asp showed nearly identical mass adducts, arguing for a similar pathway of inactivation. Molecular modeling shows that novel electrostatic interactions are formed between Arg244Nη2 and both 276AspOδ1 and Oδ2; these new forces restrict the spatial position of Arg244, a residue important in the recognition of the C3/C4 carboxylate of β-lactam substrates and inhibitors. Testing the functional consequences of this interaction, we noted considerable free energy costs (+ΔΔG) for substrates and inhibitors. A rigid carbapenem (meropenem) was most affected by the Asn276Asp substitution (46-fold increase in Ki vs SHV-1). We conclude that residue 276 is an important second-shell residue in class A β-lactamase-mediated resistance to substrates and inhibitors, and only Asn is able to precisely modulate the conformational flexibility of Arg244 required for successful evolution in nature. PMID:19351161

  20. Site-directed mutagenesis of amino acid residues of D1 protein interacting with phosphatidylglycerol affects the function of plastoquinone QB in photosystem II.

    PubMed

    Endo, Kaichiro; Mizusawa, Naoki; Shen, Jian-Ren; Yamada, Masato; Tomo, Tatsuya; Komatsu, Hirohisa; Kobayashi, Masami; Kobayashi, Koichi; Wada, Hajime

    2015-12-01

    Recent X-ray crystallographic analysis of photosystem (PS) II at 1.9-Å resolution identified 20 lipid molecules in the complex, five of which are phosphatidylglycerol (PG). In this study, we mutagenized amino acid residues S232 and N234 of D1, which interact with two of the PG molecules (PG664 and PG694), by site-directed mutagenesis in Synechocystis sp. PCC 6803 to investigate the role of the interaction in PSII. The serine and asparagine residues at positions 232 and 234 from the N-terminus were mutagenized to alanine and aspartic acid, respectively, and a mutant carrying both amino acid substitutions was also produced. Although the obtained mutants, S232A, N234D, and S232AN234D, exhibited normal growth, they showed decreased photosynthetic activities and slower electron transport from QA to QB than the control strain. Thermoluminescence analysis suggested that this slower electron transfer in the mutants was caused by more negative redox potential of QB, but not in those of QA and S2. In addition, the levels of extrinsic proteins, PsbV and PsbU, were decreased in PSII monomer purified from the S232AN234D mutant, while that of Psb28 was increased. In the S232AN234D mutant, the content of PG in PSII was slightly decreased, whereas that of monogalactosyldiacylglycerol was increased compared with the control strain. These results suggest that the interactions of S232 and N234 with PG664 and PG694 are important to maintain the function of QB and to stabilize the binding of extrinsic proteins to PSII. PMID:25921208

  1. Pump-Probe Spectroscopy of Two-Body Correlations in Ultracold Gases

    SciTech Connect

    Koch, Christiane P.; Kosloff, Ronnie

    2009-12-31

    We suggest pump-probe spectroscopy to study pair correlations that determine the many-body dynamics in weakly interacting, dilute ultracold gases. A suitably chosen, short laser pulse depletes the pair density locally, creating a 'hole' in the electronic ground state. The dynamics of this nonstationary pair density is monitored by a time-delayed probe pulse. The resulting transient signal allows us to spectrally decompose the hole and to map out the pair correlation function.

  2. Maize Root Lectins Mediate the Interaction with Herbaspirillum seropedicae via N-Acetyl Glucosamine Residues of Lipopolysaccharides

    PubMed Central

    Balsanelli, Eduardo; Tuleski, Thalita Regina; de Baura, Valter Antonio; Yates, Marshall Geoffrey; Chubatsu, Leda Satie; de Oliveira Pedrosa, Fabio; de Souza, Emanuel Maltempi; Monteiro, Rose Adele

    2013-01-01

    Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization. PMID:24130823

  3. Maize root lectins mediate the interaction with Herbaspirillum seropedicae via N-acetyl glucosamine residues of lipopolysaccharides.

    PubMed

    Balsanelli, Eduardo; Tuleski, Thalita Regina; de Baura, Valter Antonio; Yates, Marshall Geoffrey; Chubatsu, Leda Satie; Pedrosa, Fabio de Oliveira; de Souza, Emanuel Maltempi; Monteiro, Rose Adele

    2013-01-01

    Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization. PMID:24130823

  4. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2001-2002 Annual Report.

    SciTech Connect

    Pearsons, Todd N.; James, Brenda B.; Johnson, Christopher L.

    2003-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation is working or not working (Busack et al

  5. Mutation of a single residue, β-glutamate-20, alters protein–lipid interactions of light harvesting complex II

    PubMed Central

    Kwa, Lee Gyan; Wegmann, Dominik; Brügger, Britta; Wieland, Felix T; Wanner, Gerhard; Braun, Paula

    2008-01-01

    It is well established that assembly of the peripheral antenna complex, LH2, is required for proper photosynthetic membrane biogenesis in the purple bacterium Rhodobacter sphaeroides. The underlying interactions are, as yet, not understood. Here we examined the relationship between the morphology of the photosynthetic membrane and the lipid–protein interactions at the LH2–lipid interface. The non-bilayer lipid, phosphatidylethanolamine, is shown to be highly enriched in the boundary lipid phase of LH2. Sequence alignments indicate a putative lipid binding site, which includes β-glutamate-20 and the adjacent carotenoid end group. Replacement of β-glutamate-20 with alanine results in significant reduction of phosphatidylethanolamine and concomitant raise in phosphatidylcholine in the boundary lipid phase of LH2 without altering the lipid composition of the bulk phase. The morphology of the LH2 housing membrane is, however, unaffected by the amino acid replacement. In contrast, simultaneous modification of glutamate-20 and exchange of the carotenoid sphaeroidenone with neurosporene results in significant enlargement of the vesicular membrane invaginations. These findings suggest that the LH2 complex, specifically β-glutamate-20 and the carotenoids' polar head group, contribute to the shaping of the photosynthetic membrane by specific interactions with surrounding lipid molecules. PMID:18034796

  6. Two-body pion absorption on {sup 3}He at threshold

    SciTech Connect

    Lee, T.S.H.; Kiang, L.L.; Riska, D.O.

    1995-08-01

    We showed that a drastic reduction of the ratio of the rates of the reactions {sup 3}He({pi}{sup -},nn) and {sup 3}He({pi}{sup -},np) for stopped pions is obtained once the effect of the short-range two-nucleon components of the axial charge operator for nuclear systems is taken into account. In a calculation using realistic models of nucleon-nucleon interactions in the construction of these short-range components of the axial charge operator, the predicted ratios can be brought to within 10-20% of the empirical value. A paper describing our results was published.

  7. The One-Body and Two-Body Density Matrices of Finite Nuclei and Center-of-Mass Correlations

    SciTech Connect

    Shebeko, A.; Papakonstantinou, P.; Mavrommatis, E.

    2006-04-26

    A method is presented for the calculation of the one-body (1DM) and two-body (2DM) density matrices and their Fourier transforms in momentum space, that is consistent with the requirement for translational invariance (TI), in the case of a nucleus (a finite self-bound system). We restore TI by using the so-called fixed center-of-mass (CM) approximation for constructing an intrinsic nuclear ground state wavefunction (WF) by starting from a non-translationally invariant (nTI) WF and applying a projection prescription. We discuss results for the one-body (OBMD) and two-body (TBMD) momentum distributions of the 4He nucleus calculated with the Slater determinant of the harmonic oscillator (HO) orbitals, as the initial nTI WF. Effects of such an inclusion of CM correlations are found to be quite important in the momentum distributions.

  8. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.

    PubMed

    Stetz, Gabrielle; Verkhivker, Gennady M

    2016-08-22

    Although molecular mechanisms of allosteric regulation in the Hsp70 chaperones have been extensively studied at both structural and functional levels, the current understanding of allosteric inhibition of chaperone activities by small molecules is still lacking. In the current study, using a battery of computational approaches, we probed allosteric inhibition mechanisms of E. coli Hsp70 (DnaK) and human Hsp70 proteins by small molecule inhibitors PET-16 and novolactone. Molecular dynamics simulations and binding free energy analysis were combined with network-based modeling of residue interactions and allosteric communications to systematically characterize and compare molecular signatures of the apo form, substrate-bound, and inhibitor-bound chaperone complexes. The results suggested a mechanism by which the allosteric inhibitors may leverage binding energy hotspots in the interaction networks to stabilize a specific conformational state and impair the interdomain allosteric control. Using the network-based centrality analysis and community detection, we demonstrated that substrate binding may strengthen the connectivity of local interaction communities, leading to a dense interaction network that can promote an efficient allosteric communication. In contrast, binding of PET-16 to DnaK may induce significant dynamic changes and lead to a fractured interaction network and impaired allosteric communications in the DnaK complex. By using a mechanistic-based analysis of distance fluctuation maps and allosteric propensities of protein residues, we determined that the allosteric network in the PET-16 complex may be small and localized due to the reduced communication and low cooperativity of the substrate binding loops, which may promote the higher rates of substrate dissociation and the decreased substrate affinity. In comparison with the significant effect of PET-16, binding of novolactone to HSPA1A may cause only moderate network changes and preserve allosteric

  9. The Two-Body Problem in the Point Mass Approximation Field. II. Escape and Near-Escape Dynamics

    NASA Astrophysics Data System (ADS)

    Mioc, Vasile; Stavinschi, Magda

    The study of the two-body problem in the point mass approximation field (featured by the potential A/r+Br2, with r=distance between particles, and A, B=real nonzero constants) is continued by tackling the situation r→∞. The infinity singularity is blown up via McGehee-type transformations, and the infinity manifold is pasted on the phase space. The fictitious flow on this manifold is described, and the local flow near infinity, too.

  10. Development of a two-body wet abrasion test method with attention to the effects of reused abradant

    SciTech Connect

    Blau, Peter Julian; Dehoff, Ryan R

    2012-01-01

    Abrasive wear is among the most common and costliest causes for material wastage, and it occurs in many forms. A simple method has been developed to quantify the response of metals and alloys to two-body wet abrasion. A metallographic polishing machine was modified to create a disk-on-flat sliding test rig. Adhesive-backed SiC grinding papers were used under fixed load and speed to rank the abrasive wear of seven alloy steels, some of which are candidates for drill cones for geothermal drilling. Standardized two-body abrasion tests, like those described in ASTM G132, feed unused abrasive into the contact; however, the current work investigated whether useful rankings could still be obtained with a simpler testing configuration in which specimens repeatedly slide on the same wear path under water-lubricated conditions. Tests using abrasive grit sizes of 120 and 180 resulted in the same relative ranking of the alloys although the coarser grit produced more total wear. Wear decreased when the same abrasive disk was re-used for up to five runs, but the relative rankings of the steels remained the same. This procedure was presented to ASTM Committee G2 on Wear and Erosion as a potential standard test for wet two-body abrasive wear.