Enzyme-catalyzed uridine phosphorolysis: SN2 mechanism with phosphate activation by desolvation

AbstractThe rate of uridine phosphorolysis catalyzed by uridine phosphorylase from Escherichia coli decreases with increasing ionic strength. In contrast, the rate was increased about twofold after preincubation of uridine phosphorylase with 60% acetonitrile. These data correlate with known effects of polar and bipolar aprotic solvents on SN2 nucleophilic substitution reactions. The enzyme modified with fluorescein-5′-isothiocyanate (fluorescein residue occupies an uridine-binding subsite [Komissarov et al., (1994) Biochim. Biophys. Acta 1205, 54–58]) was selectively modified with irreversible inhibitor SA-423, which reacts near the phosphate-binding subsite. The double-modified uridine phosphorylase is assumed to imitate the enzyme—substrate complex. Modification with SA-423 was accompanied with dramatic changes in the absorption spectrum of active site-linked fluorescein, which were identical to those for fluorescein in a hydrophobic medium, namely 80% acetonitrile. The data obtained suggest that an increase in active site hydrophobicity leads to phosphate desolvation and facilitates the enzymatic SN2 uridine phosphorolysis reaction

Electronic Structure and X-Ray Photoelectron Spectra of Some Perovskite Molecular Crystals

It is new study of some molecular crystals with a perovskite structure, whose luminescent, thermochromic, nonlinear optical and dielectric properties provide opportunities for their wide practical application. This paper presents the results of an investigation of the electronic structure and the orbital nature of crystals with the AMX6 formula (where A = Cs, HGu; M = Te, Sb, Ir, Os, Re, W; X = F, Cl, Br). The electronic structure of crystals with Te and Sb atoms was determined by the method of X-ray photoelectron spectroscopy and quantum-chemical modeling within the framework of the density functional theory. We identified the molecular orbitals which are responsible for covalent metal-halogen binding. Also we found that the transition from the 3a1g highest occupied molecular orbital to the 4t1u lowest unoccupied molecular orbital, which corresponds to the states 1T1u and 3T1u, is responsible for the luminescence of the [MX6] 2– anions

Atomic structure at 2.5 Å resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice

AbstractUridine phosphorylase from E. coli (Upase) has been crystallized using vapor diffusion technique in a new monoclinic crystal form. The structure was determined by the molecular replacement method at 2.5 Å resolution. The coordinates of the trigonal crystal form were used as a starting model and the refinement by the program XPLOR led to the R-factor of 18.6%. The amino acid fold of the protein was found to be the same as that in the trigonal crystals. The positions of flexible regions were refined. The conclusion about the involvement in the active site is in good agreement with the results of the biochemical experiments

Magnetoluminescence

Pulsar Wind Nebulae, Blazars, Gamma Ray Bursts and Magnetars all contain regions where the electromagnetic energy density greatly exceeds the plasma energy density. These sources exhibit dramatic flaring activity where the electromagnetic energy distributed over large volumes, appears to be converted efficiently into high energy particles and gamma-rays. We call this general process magnetoluminescence. Global requirements on the underlying, extreme particle acceleration processes are described and the likely importance of relativistic beaming in enhancing the observed radiation from a flare is emphasized. Recent research on fluid descriptions of unstable electromagnetic configurations are summarized and progress on the associated kinetic simulations that are needed to account for the acceleration and radiation is discussed. Future observational, simulation and experimental opportunities are briefly summarized.Comment: To appear in "Jets and Winds in Pulsar Wind Nebulae, Gamma-ray Bursts and Blazars: Physics of Extreme Energy Release" of the Space Science Reviews serie

Particle Acceleration in Pulsar Wind Nebulae: PIC modelling

We discuss the role of particle-in-cell (PIC) simulations in unveiling the origin of the emitting particles in PWNe. After describing the basics of the PIC technique, we summarize its implications for the quiescent and the flaring emission of the Crab Nebula, as a prototype of PWNe. A consensus seems to be emerging that, in addition to the standard scenario of particle acceleration via the Fermi process at the termination shock of the pulsar wind, magnetic reconnection in the wind, at the termination shock and in the Nebula plays a major role in powering the multi-wavelength signatures of PWNe.Comment: 32 pages, 16 figures, to appear in the book "Modelling Nebulae" edited by D. Torres for Springer, based on the invited contributions to the workshop held in Sant Cugat (Barcelona), June 14-17, 201

Magnetic fields in supernova remnants and pulsar-wind nebulae

We review the observations of supernova remnants (SNRs) and pulsar-wind nebulae (PWNe) that give information on the strength and orientation of magnetic fields. Radio polarimetry gives the degree of order of magnetic fields, and the orientation of the ordered component. Many young shell supernova remnants show evidence for synchrotron X-ray emission. The spatial analysis of this emission suggests that magnetic fields are amplified by one to two orders of magnitude in strong shocks. Detection of several remnants in TeV gamma rays implies a lower limit on the magnetic-field strength (or a measurement, if the emission process is inverse-Compton upscattering of cosmic microwave background photons). Upper limits to GeV emission similarly provide lower limits on magnetic-field strengths. In the historical shell remnants, lower limits on B range from 25 to 1000 microGauss. Two remnants show variability of synchrotron X-ray emission with a timescale of years. If this timescale is the electron-acceleration or radiative loss timescale, magnetic fields of order 1 mG are also implied. In pulsar-wind nebulae, equipartition arguments and dynamical modeling can be used to infer magnetic-field strengths anywhere from about 5 microGauss to 1 mG. Polarized fractions are considerably higher than in SNRs, ranging to 50 or 60% in some cases; magnetic-field geometries often suggest a toroidal structure around the pulsar, but this is not universal. Viewing-angle effects undoubtedly play a role. MHD models of radio emission in shell SNRs show that different orientations of upstream magnetic field, and different assumptions about electron acceleration, predict different radio morphology. In the remnant of SN 1006, such comparisons imply a magnetic-field orientation connecting the bright limbs, with a non-negligible gradient of its strength across the remnant.Comment: 20 pages, 24 figures; to be published in SpSciRev. Minor wording change in Abstrac

Magnetic Reconnection in Extreme Astrophysical Environments

Magnetic reconnection is a basic plasma process of dramatic rearrangement of magnetic topology, often leading to a violent release of magnetic energy. It is important in magnetic fusion and in space and solar physics --- areas that have so far provided the context for most of reconnection research. Importantly, these environments consist just of electrons and ions and the dissipated energy always stays with the plasma. In contrast, in this paper I introduce a new direction of research, motivated by several important problems in high-energy astrophysics --- reconnection in high energy density (HED) radiative plasmas, where radiation pressure and radiative cooling become dominant factors in the pressure and energy balance. I identify the key processes distinguishing HED reconnection: special-relativistic effects; radiative effects (radiative cooling, radiation pressure, and Compton resistivity); and, at the most extreme end, QED effects, including pair creation. I then discuss the main astrophysical applications --- situations with magnetar-strength fields (exceeding the quantum critical field of about 4 x 10^13 G): giant SGR flares and magnetically-powered central engines and jets of GRBs. Here, magnetic energy density is so high that its dissipation heats the plasma to MeV temperatures. Electron-positron pairs are then copiously produced, making the reconnection layer highly collisional and dressing it in a thick pair coat that traps radiation. The pressure is dominated by radiation and pairs. Yet, radiation diffusion across the layer may be faster than the global Alfv\'en transit time; then, radiative cooling governs the thermodynamics and reconnection becomes a radiative transfer problem, greatly affected by the ultra-strong magnetic field. This overall picture is very different from our traditional picture of reconnection and thus represents a new frontier in reconnection research.Comment: Accepted to Space Science Reviews (special issue on magnetic reconnection). Article is based on an invited review talk at the Yosemite-2010 Workshop on Magnetic Reconnection (Yosemite NP, CA, USA; February 8-12, 2010). 30 pages, no figure

Gluon polarization in the nucleon from quasi-real photoproduction of high-pT hadron pairs

We present a determination of the gluon polarization Delta G/G in the nucleon, based on the helicity asymmetry of quasi-real photoproduction events, Q^2<1(GeV/c)^2, with a pair of large transverse-momentum hadrons in the final state. The data were obtained by the COMPASS experiment at CERN using a 160 GeV polarized muon beam scattered on a polarized 6-LiD target. The helicity asymmetry for the selected events is = 0.002 +- 0.019(stat.) +- 0.003(syst.). From this value, we obtain in a leading-order QCD analysis Delta G/G=0.024 +- 0.089(stat.) +- 0.057(syst.) at x_g = 0.095 and mu^2 =~ 3 (GeV}/c)^2.Comment: 10 pages, 3 figure

The Deuteron Spin-dependent Structure Function g1d and its First Moment

We present a measurement of the deuteron spin-dependent structure function g1d based on the data collected by the COMPASS experiment at CERN during the years 2002-2004. The data provide an accurate evaluation for Gamma_1^d, the first moment of g1d(x), and for the matrix element of the singlet axial current, a0. The results of QCD fits in the next to leading order (NLO) on all g1 deep inelastic scattering data are also presented. They provide two solutions with the gluon spin distribution function Delta G positive or negative, which describe the data equally well. In both cases, at Q^2 = 3 (GeV/c)^2 the first moment of Delta G is found to be of the order of 0.2 - 0.3 in absolute value.Comment: fits redone using MRST2004 instead of MRSV1998 for G(x), correlation matrix adde