Structure of a new crystal form of 2-{[3-(trifluoromethyl)phenyl]amino}benzoic acid (flufenamic acid)

C14Ht0F3NO2, P2.Jc, a = 12.523 (4), b = 7.868(6), c = 12.874 (3)A, fl = 95.2 (2) ° , O,,, = 1.47 (4), D e = 1.47 Mg m -3, Z = 4. Final R = 0.074 for 2255 observed reflections. The carboxyl group and the phenyl ring bearing the carboxyl group are nearly coplanar whereas the two phenyl rings are inclined with respect to each other at 52.8 ° . The difference between the two polymorphs of flufenamic acid lies in the geometrical disposition of the [3-(trifluoromethyl)- phenyl]amino moiety with respect to the benzoic acid moiety. As in other fenamate structures, the carboxyl group and the imino N atom are connected through an intramolecular hydrogen bond; also, pairs of centrosymmetrically related molecules are connected through hydrogen bonds involving carboxyl groups.

The Mycobacterial MsDps2 Protein Is a Nucleoid-Forming DNA Binding Protein Regulated by Sigma Factors sigma(A) and sigma(B)

The Dps (DNA-binding protein from starved cells) proteins from Mycobacterium smegmatis MsDps1 and MsDps2 are both DNA-binding proteins with some differences. While MsDps1 has two oligomeric states, with one of them responsible for DNA binding, MsDps2 has only one DNA-binding oligomeric state. Both the proteins however, show iron-binding activity. The MsDps1 protein has been shown previously to be induced under conditions of starvation and osmotic stress and is regulated by the extra cellular sigma factors sigma(H) and sigma(F). We show here, that the second Dps homologue in M. smegmatis, namely MsDps2, is purified in a DNA-bound form and exhibits nucleoid-like structures under the atomic force microscope. It appears that the N-terminal sequence of Dps2 plays a role in nucleoid formation. MsDps2, unlike MsDps1, does not show elevated expression in nutritionally starved or stationary phase conditions; rather its promoter is recognized by RNA polymerase containing sigma(A) or sigma(B), under in vitro conditions. We propose that due to the nucleoid-condensing ability, the expression of MsDps2 is tightly regulated inside the cells.

Surface cathepsin B protects cytotoxic lymphocytes from self-destruction after degranulation.

The granule exocytosis cytotoxicity pathway is the major molecular mechanism for cytotoxic T lymphocyte (CTL) and natural killer (NK) cytotoxicity, but the question of how these cytotoxic lymphocytes avoid self-destruction after secreting perforin has remained unresolved. We show that CTL and NK cells die within a few hours if they are triggered to degranulate in the presence of nontoxic thiol cathepsin protease inhibitors. The potent activity of the impermeant, highly cathepsin B-specific membrane inhibitors CA074 and NS-196 strongly implicates extracellular cathepsin B. CTL suicide in the presence of cathepsin inhibitors requires the granule exocytosis cytotoxicity pathway, as it is normal with CTLs from gld mice, but does not occur in CTLs from perforin knockout mice. Flow cytometry shows that CTLs express low to undetectable levels of cathepsin B on their surface before degranulation, with a substantial rapid increase after T cell receptor triggering. Surface cathepsin B eluted from live CTL after degranulation by calcium chelation is the single chain processed form of active cathepsin B. Degranulated CTLs are surface biotinylated by the cathepsin B-specific affinity reagent NS-196, which exclusively labels immunoreactive cathepsin B. These experiments support a model in which granule-derived surface cathepsin B provides self-protection for degranulating cytotoxic lymphocytes.

Stringent constraints on the scalar K pi form factor from analyticity, unitarity and low-energy theorems

We investigate the scalar K pi form factor at low energies by the method of unitarity bounds adapted so as to include information on the phase and modulus along the elastic region of the unitarity cut. Using at input the values of the form factor at t = 0 and the Callan-Treiman point, we obtain stringent constraints on the slope and curvature parameters of the Taylor expansion at the origin. Also, we predict a quite narrow range for the higher-order ChPT corrections at the second Callan-Treiman point.

Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Theory of unitarity bounds and low-energy form factors

We present a general formalism for deriving bounds on the shape parameters of the weak and electromagnetic form factors using as input correlators calculated from perturbative QCD, and exploiting analyticity and unitarily. The values resulting from the symmetries of QCD at low energies or from lattice calculations at special points inside the analyticity domain can be included in an exact way. We write down the general solution of the corresponding Meiman problem for an arbitrary number of interior constraints and the integral equations that allow one to include the phase of the form factor along a part of the unitarity cut. A formalism that includes the phase and some information on the modulus along a part of the cut is also given. For illustration we present constraints on the slope and curvature of the K-l3 scalar form factor and discuss our findings in some detail. The techniques are useful for checking the consistency of various inputs and for controlling the parameterizations of the form factors entering precision predictions in flavor physics.

Interior Medial Axis Transform computation of 3D objects bound by free-form surfaces

This paper presents an algorithm for generating the Interior Medial Axis Transform (iMAT) of 3D objects with free-form boundaries. The algorithm proposed uses the exact representation of the part and generates an approximate rational spline description of the iMAT. The algorithm generates the iMAT by a tracing technique that marches along the object's boundary. The level of approximation is controlled by the choice of the step size in the tracing procedure. Criteria based on distance and local curvature of boundary entities are used to identify the junction points and the search for these junction points is done in an efficient way. The algorithm works for multiply-connected objects as well. Results of the implementation are provided. (C) 2010 Elsevier Ltd. All rights reserved.

Improving the phenomenology of Kl3 form factors with analyticity and unitarity

The shape of the vector and scalar K-l3 form factors is investigated by exploiting analyticity and unitarity in a model-independent formalism. The method uses as input dispersion relations for certain correlators computed in perturbative QCD in the deep Euclidean region, soft-meson theorems, and experimental information on the phase and modulus of the form factors along the elastic part of the unitarity cut. We derive constraints on the coefficients of the parameterizations valid in the semileptonic range and on the truncation error. The method also predicts low-energy domains in the complex t plane where zeros of the form factors are excluded. The results are useful for K-l3 data analyses and provide theoretical underpinning for recent phenomenological dispersive representations for the form factors.

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

Lipid-amphotericin B complex structure in solution: A possible first step in the aggregation process in cell membranes

The interactions between the polyene antibiotic amphotericin B with dipalmitoylphosphatidylcholine were investigated in vesicles (using circular dichroism) and in chloroform solution (using circular dichroism and IH, I3C, and 31P nuclear magnetic resonance). The results show that amphotericin B readily aggregates in vesicles and that the extent of aggregation depends on the 1ipid:drug concentration ratio. Introduction of sterol molecules into the membrane hastens the process of aggregation of amphotericin B. In chloroform solutions amphotericin B strongly interacts with phospholipid molecules to form a stoichiometric complex. The results suggest that there are interactions between the conjugated heptene stretch of amphotericin B and the methylene groups of lipid acyl chains, while the sugar moiety interacts with the phosphate head group by the formation of a hydrogen bond. A model is proposed for the lipid-amphotericin B complex, in which amphotericin B interacts equally well with the two lipid acyl chains, forming a 1:l complex.

Implications of the recent high statistics determination of the pion electromagnetic form factor in the timelike region

The recently evaluated two-pion contribution to the muon g - 2 and the phase of the pion electromagnetic form factor in the elastic region, known from pi pi scattering by Fermi-Watson theorem, are exploited by analytic techniques for finding correlations between the coefficients of the Taylor expansion at t = 0 and the values of the form factor at several points in the spacelike region. We do not use specific parametrizations, and the results are fully independent of the unknown phase in the inelastic region. Using for instance, from recent determinations, < r(pi)(2)> = (0.435 +/- 0.005) fm(2) and F(-1.6 GeV2) = 0.243(-0.014)(+0.022), we obtain the allowed ranges 3.75 GeV-4 less than or similar to c less than or similar to 3.98 GeV-4 and 9.91 GeV-6 less than or similar to d less than or similar to 10.46 GeV-6 for the curvature and the next Taylor coefficient, with a strong correlation between them. We also predict a large region in the complex plane where the form factor cannot have zeros.

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form

The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 Angstrom resolution The final R factor is 19.74b for all data in the resolution range 8.0-2.3 Angstrom. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI wi th methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which an hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 Angstrom of the main-chain atoms of the variable loop.

Mapping of B-cell epitopes of hemagglutinin protein of rinderpest virus

Monoclonal antibodies (mAbs) against secreted hemagglutinin (H) protein of rinderpest virus (RPV) expressed by a recombinant baculovirus were generated to characterize the antigenic sites on H protein and regions of functional significance. Three of the mAbs displayed hemagglutination inhibition activity and these mAbs were unable to neutralize virus infectivity. Western immunoblot analysis of overlapping deletion mutants indicated that three mAbs recognize antigenic regions at the extreme carboxy terminus (between amino acids 569 and 609) and the fourth mAb between amino acids 512 and 568. Using synthetic peptides, aa 569-577 and 575-583 were identified as the epitopes for E2G4 and D2F4, respectively. The epitopic domains of A12A9 and E2B6 mAbs were mapped to regions encompassing aa 527-554 and 588-609. Two epitopes spanning the extreme carboxy terminal region of aa 573 to 587 and 588 to 609 were shown to be immunodominant employing a competitive ELISA with polyclonal sera form vaccinated cattle. The D2F4 mAb which recognizes a unique epitope on RPV-H is not present on the closely related peste des petits ruminant virus FIN protein and this mAb could serve as a tool in the seromonitoring program after rinderpest vaccination. (C) 2002 Elsevier Science (USA).

Structural model for the Cu-B site of dopamine beta-hydroxylase: Crystal structure of a copper(II) complex showing N3OS coordination with an axial sulfur ligation

A copper(II) complex containing a NSO-donor Schiff base and NN-donor 2,2'-bipyridine has been prepared and structurally characterized. The square pyramidal complex with an axial sulfur ligation is a structural model for the CUB site of dopamine-hydroxylase in its oxidized form. The copper(II) complex is catalytically active in the oxidation of ascorbic acid by dioxygen mediated by a copper(I) species which is proposed to have a four-coordinate structure with a N3S coordination geometry.

Implications of unitarity and analyticity for the D pi form factors

We consider the vector and scalar form factors of the charm-changing current responsible for the semileptonic decay D -> pi/nu. Using as input dispersion relations and unitarity for the moments of suitable heavy-light correlators evaluated with Operator Product Expansions, including O(alpha(2)(s)) terms in perturbative QCD, we constrain the shape parameters of the form factors and find exclusion regions for zeros on the real axis and in the complex plane. For the scalar form factor, a low-energy theorem and phase information on the unitarity cut are also implemented to further constrain the shape parameters. We finally propose new analytic expressions for the D pi form factors, derive constraints on the relevant coefficients from unitarity and analyticity, and briefly discuss the usefulness of the new parametrizations for describing semileptonic data.