QCD sum rules with finite masses

The concept of QCD sum rules is extended to bound states composed of particles with finite mass such as scalar quarks or strange quarks. It turns out that mass corrections become important in this context. The number of relevant corrections is analyzed in a systematic discussion of the IR- and UV-divergencies, leading in general to a finite number of corrections. The results are demonstrated for a system of two massless quarks and two heavy scalar quarks.Comment: 15 pages, including two pictures to be found in an extra file. Latex neads epsf.st

COALESCING NEUTRON STARS AS GAMMA RAY BURSTERS ?

We investigate the dynamics and evolution of coalescing neutron stars. The three-dimensional Newtonian equations of hydrodynamics are integrated by the `Piecewise Parabolic Method' However, we do include the effects of the emission of gravitational waves on the hydrodynamics. The properties of neutron star matter are described by the equation of state of Lattimer & Swesty. In addition to the fundamental hydrodynamic quantities, density, momentum, and energy, we follow the time evolution of the electron density in the stellar gas. Energy losses and changes of the electron abundance due to the emission of neutrinos are taken into account by an elaborate ``neutrino leakage scheme'', which employs a careful calculation of the lepton number and energy source terms of all neutrino types. The grid is Cartesian and equidistant with a resolution of 64**3 or 128**3, which allows us to calculate the self-gravity via fast Fourier transforms.Comment: extended abstract contribution to the proceedings of the 17th Texas Symposium, 2 pages, uuencoded compressed postscript

Correlation functions of scattering matrix elements in microwave cavities with strong absorption

The scattering matrix was measured for microwave cavities with two antennas. It was analyzed in the regime of overlapping resonances. The theoretical description in terms of a statistical scattering matrix and the rescaled Breit-Wigner approximation has been applied to this regime. The experimental results for the auto-correlation function show that the absorption in the cavity walls yields an exponential decay. This behavior can only be modeled using a large number of weakly coupled channels. In comparison to the auto-correlation functions, the cross-correlation functions of the diagonal S-matrix elements display a more pronounced difference between regular and chaotic systems

Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae

EndA is a membrane-attached surface-exposed DNA-entry nuclease previously known to be required for genetic transformation of Streptococcus pneumoniae. More recent studies have shown that the enzyme also plays an important role during the establishment of invasive infections by degrading extracellular chromatin in the form of neutrophil extracellular traps (NETs), enabling streptococci to overcome the innate immune system in mammals. As a virulence factor, EndA has become an interesting target for future drug design. Here we present the first mutational and biochemical analysis of recombinant forms of EndA produced either in a cell-free expression system or in Escherichia coli. We identify His160 and Asn191 to be essential for catalysis and Asn182 to be required for stability of EndA. The role of His160 as the putative general base in the catalytic mechanism is supported by chemical rescue of the H160A variant of EndA with imidazole added in excess. Our study paves the way for the identification and development of protein or low-molecular-weight inhibitors for EndA in future high-throughput screening assays

A series of PDB related databases for everyday needs

The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design

Structural and functional characterization of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in l-lactate and sugar utilization

LldR (CGL2915) from Corynebacterium glutamicum is a transcription factor belonging to the GntR family, which is typically involved in the regulation of oxidized substrates associated with amino acid metabolism. In the present study, the crystal structure of LldR was determined at 2.05-Å resolution. The structure consists of N- and C-domains similar to those of FadR, but with distinct domain orientations. LldR and FadR dimers achieve similar structures by domain swapping, which was first observed in dimeric assembly of transcription factors. A structural feature of Zn2+ binding in the regulatory domain was also observed, as a difference from the FadR subfamily. DNA microarray and DNase I footprint analyses suggested that LldR acts as a repressor regulating cgl2917-lldD and cgl1934-fruK-ptsF operons, which are indispensable for l-lactate and fructose/sucrose utilization, respectively. Furthermore, the stoichiometries and affinities of LldR and DNAs were determined by isothermal titration calorimetry measurements. The transcriptional start site and repression of LldR on the cgl2917-lldD operon were analysed by primer extension assay. Mutation experiments showed that residues Lys4, Arg32, Arg42 and Gly63 are crucial for DNA binding. The location of the putative ligand binding cavity and the regulatory mechanism of LldR on its affinity for DNA were proposed

A Critical Analysis of the Proton Form Factor with Sudakov Suppression and Intrinsic Transverse Momentum

The behavior of the proton magnetic form factor is studied within the modified hard scattering picture, which takes into account gluonic radiative corrections in terms of transverse separations. We parallel the analysis given previously by Li and make apparent a number of serious objections. The appropriate cut-off needed to render the form-factor calculation finite is both detailed and analyzed by considering different cut-off prescriptions. The use of the maximum interquark separation as a common infrared cut-off in the Sudakov suppression factor is proposed, since it avoids difficulties with the $\alpha _{s}$-singularities and yields a proton form factor insensitive to the inclusion of the soft region which therefore can be confidently attributed to perturbative QCD. Results are presented for a variety of proton wave functions including also their intrinsic transverse momentum. It turns out that the perturbative contribution, although theoretically self-consistent for $Q^{2}$ larger than about $6$~GeV${}^{2}$ to $10$~GeV${}^{2}$, is too small compared to the data.Comment: 31 pages (RevTex) + 6 figures in PS-file; preprint BUGH Wuppertal WU-B-94-06, preprint Ruhr-Universit\"at Bochum RUB-TPII-01/9