Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 Å resolution

The three-dimensional structure of the R form of rabbit liver fructose 1,6-bisphosphatase (Fru-1,6-Pase; E.C. 3.1.3.11) has been determined by a combination of heavy-atom and molecular-replacement methods. A model, which includes 2394 protein atoms and 86 water molecules, has been refined at 2.3 Å resolution to a crystallographic R factor of 0.177. The root-mean-square deviations of bond distances and angles from standard geometry are 0.012 Å and 1.7°, respectively. This structural result, in conjunction with recently redetermined amino-acid sequence data, unequivocally establishes that the rabbit liver enzyme is not an aberrant bisphosphatase as once believed, but is indeed homologous to other Fru-1,6-Pases. The root-mean-square deviation of the C atoms in the rabbit liver structure from the homologous atoms in the pig kidney structure complexed with the product, fructose 6-phosphate, is 0.7 Å. Fru-1,6-Pases are homotetramers, and the rabbit liver protein crystallizes in space group I222 with one monomer in the asymmetric unit. The structure contains a single endogenous Mg<sup>2+</sup> ion coordinated by Glu97, Asp118, Asp121 and Glu280 at the site designated metal site 1 in pig kidney Fru-1,6-Pase R-form complexes. In addition, two sulfate ions, which are found at the positions normally occupied by the 6-phosphate group of the substrate, as well as the phosphate of the allosteric inhibitor AMP appear to provide stability. Met177, which has hydrophobic contacts with the adenine moiety of AMP in pig kidney T-form complexes, is replaced by glycine. Binding of a non-hydrolyzable substrate analog,<sup> β</sup>-methyl-fructose 1,6-bisphosphate, at the catalytic site is also examined

Convergence rates of posterior distributions.

We consider the asymptotic behavior of posterior distributions and Bayes estimators for infinite-dimensional statistical models. We give general results on the rate of convergence of the posterior measure. These are applied to several examples, including priors on finite sieves, log-spline models, Dirichlet processes and interval censoring

Chiral corrections in hadron spectroscopy

We show that the implementation of chiral symmetry in recent studies of the hadron spectrum in the context of the constituent quark model is inconsistent with chiral perturbation theory. In particular, we show that the leading nonanalytic (LNA) contributions to the hadron masses are incorrect in such approaches. The failure to implement the correct chiral behaviour of QCD results in incorrect systematics for the corrections to the masses.Comment: 7 pages, latex, 1 eps figure, version to appear in Phys. Lett.

Breaking of general rotational symmetries by multi-dimensional classical ratchets

We demonstrate that a particle driven by a set of spatially uncorrelated, independent colored noise forces in a bounded, multidimensional potential exhibits rotations that are independent of the initial conditions. We calculate the particle currents in terms of the noise statistics and the potential asymmetries by deriving an n-dimensional Fokker-Planck equation in the small correlation time limit. We analyze a variety of flow patterns for various potential structures, generating various combinations of laminar and rotational flows.Comment: Accepted, Physical Review

Complete Break Up of Ortho Positronium (Ps)- Hydrogenic ion System

The dynamics of the complete breakup process in an Ortho Ps - He+ system including electron loss to the continuum (ELC) is studied where both the projectile and the target get ionized. The process is essentially a four body problem and the present model takes account of the two centre effect on the electron ejected from the Ps atom which is crucial for a proper description of the ELC phenomena. The calculations are performed in the framework of Coulomb Distorted Eikonal Approximation. The exchange effect between the target and the projectile electron is taken into account in a consistent manner. The proper asymptotic 3-body boundary condition for this ionization process is also satisfied in the present model. A distinct broad ELC peak is noted in the fully differential cross sections (5DCS) for the Ps electron corroborating qualitatively the experiment for the Ps - He system. Both the dynamics of the ELC from the Ps and the ejected electron from the target He+ in the FDCS are studied using coplanar geometry. Interesting features are noted in the FDCS for both the electrons belonging to the target and the projectile.Comment: 14 pages,7 figure

Warm stellar matter with deconfinement: application to compact stars

We investigate the properties of mixed stars formed by hadronic and quark matter in $\beta$-equilibrium described by appropriate equations of state (EOS) in the framework of relativistic mean-field theory. We use the non- linear Walecka model for the hadron matter and the MIT Bag and the Nambu-Jona-Lasinio models for the quark matter. The phase transition to a deconfined quark phase is investigated. In particular, we study the dependence of the onset of a mixed phase and a pure quark phase on the hyperon couplings, quark model and properties of the hadronic model. We calculate the strangeness fraction with baryonic density for the different EOS. With the NJL model the strangeness content in the mixed phase decreases. The calculations were performed for T=0 and for finite temperatures in order to describe neutron and proto-neutron stars. The star properties are discussed. Both the Bag model and the NJL model predict a mixed phase in the interior of the star. Maximum allowed masses for proto-neutron stars are larger for the NJL model ($\sim 1.9$ M$_{\bigodot}$) than for the Bag model ($\sim 1.6$ M$_{\bigodot}$).Comment: RevTeX,14 figures, accepted to publication in Physical Review

Stability of the lattice formed in first-order phase transitions to matter containing strangeness in protoneutron stars

Well into the deleptonization phase of a core collapse supernova, a first-order phase transition to matter with macroscopic strangeness content is assumed to occur and lead to a structured lattice defined by negatively charged strange droplets. The lattice is shown to crystallize for expected droplet charges and separations at temperatures typically obtained during the protoneutronstar evolution. The melting curve of the lattice for small spherical droplets is presented. The one-component plasma model proves to be an adequate description for the lattice in its solid phase with deformation modes freezing out around the melting temperature. The mechanical stability against shear stresses is such that velocities predicted for convective phenomena and differential rotation during the Kelvin-Helmholtz cooling phase might prevent the crystallization of the phase transition lattice. A solid lattice might be fractured by transient convection, which could result in anisotropic neutrino transport. The melting curve of the lattice is relevant for the mechanical evolution of the protoneutronstar and therefore should be included in future hydrodynamics simulations.Comment: accepted for publication in Physical Review

Holstein polarons in a strong electric field: delocalized and stretched states

The coherent dynamics of a Holstein polaron in strong electric fields is considered under different regimes. Using analytical and numerical analysis, we show that even for small hopping constant and weak electron-phonon interaction, the original discrete Wannier-Stark (WS) ladder electronic states are each replaced by a semi-continuous band if a resonance condition is satisfied between the phonon frequency and the ladder spacing. In this regime, the original localized WS states can become {\em delocalized}, yielding both `tunneling' and `stretched' polarons. The transport properties of such a system would exhibit a modulation of the phonon replicas in typical tunneling experiments. The modulation will reflect the complex spectra with nearly-fractal structure of the semi-continuous band. In the off-resonance regime, the WS ladder is strongly deformed, although the states are still localized to a degree which depends on the detuning: Both the spacing between the levels in the deformed ladder and the localization length of the resulting eigenfunctions can be adjusted by the applied electric field. We also discuss the regime beyond small hopping constant and weak coupling, and find an interesting mapping to that limit via the Lang-Firsov transformation, which allows one to extend the region of validity of the analysis.Comment: 10 pages, 13 figures, submitted to PR

On the Crustal Matter of Magnetars

We have investigated some of the properties of dense sub-nuclear matter at the crustal region (both the outer crust and the inner crust region) of a magnetar. The relativistic version of Thomas-Fermi (TF) model is used in presence of strong quantizing magnetic field for the outer crust matter. The compressed matter in the outer crust, which is a crystal of metallic iron, is replaced by a regular array of spherically symmetric Wigner-Seitz (WS) cells. In the inner crust region, a mixture of iron and heavier neutron rich nuclei along with electrons and free neutrons has been considered. Conventional Harrison-Wheeler (HW) and Bethe-Baym-Pethick (BBP) equation of states are used for the nuclear mass formula. A lot of significant changes in the characteristic properties of dense crustal matter, both at the outer crust and the inner crust, have been observed.Comment: 29 pages REVTEX manuscript, 15 .eps figures (included

Structure-function relationships of the RNA-dependent RNA polymerase from poliovirus (3Dpol): A surface of the primary oligomerization domain functions in capsid precursor processing and VPg uridylylation

The primary oligomerization domain of poliovirus polymerase, 3Dpol, is stabilized by the interaction of the back of the thumb subdomain of one molecule with the back of the palm subdomain of a second molecule, thus permitting the head-to-tail assembly of 3Dpol monomers into long fibers. The interaction of Arg-455 and Arg-456 of the thumb with Asp-339, Ser-341, and Asp-349 of the palm is key to the stability of this interface. We show that mutations predicted to completely disrupt this interface do not produce equivalent growth phenotypes. Virus encoding a polymerase with changes of both residues of the thumb to alanine is not viable; however, virus encoding a polymerase with changes of all three residues of the palm to alanine is viable. Biochemical analysis of 3Dpol derivatives containing the thumb or palm substitutions revealed that these derivatives are both incapable of forming long fibers, suggesting that polymerase fibers are not essential for virus viability. The RNA binding activity, polymerase activity, and thermal stability of these derivatives were equivalent to that of the wild-type enzyme. The two significant differences observed for the thumb mutant were a modest reduction in the ability of the altered 3CD proteinase to process the VP0/VP3 capsid precursor and a substantial reduction in the ability of the altered 3Dpol to catalyze oriI-templated uridylylation of VPg. The defect to uridylylation was a result of the inability of 3CD to stimulate this reaction. Because 3C alone can substitute for 3CD in this reaction, we conclude that the lethal replication phenotype associated with the thumb mutant is caused, in part, by the disruption of an interaction between the back of the thumb of 3Dpol and some undefined domain of 3C. We speculate that this interaction may also be critical for assembly of other complexes required for poliovirus genome replication