Analysis and mitigation of an oscillating background on hybrid complementary metal-oxide semiconductor (hCMOS) imaging sensors at the National Ignition Facility.

Nanosecond-gated hybrid complementary metal-oxide semiconductor imaging sensors are a powerful tool for temporally gated and spatially resolved measurements in high energy density science, including inertial confinement fusion, and in laser diagnostics. However, a significant oscillating background excited by photocurrent has been observed in image sequences during testing and in experiments at the National Ignition Facility (NIF). Characterization measurements and simulation results are used to explain the oscillations as the convolution of the pixel-level sensor response with a sensor-wide RLC circuit ringing. Data correction techniques are discussed for NIF diagnostics, and for diagnostics where these techniques cannot be used, a proof-of-principle image correction algorithm is presented.

The Scattered Light Time-history Diagnostic suite at the National Ignition Facility.

The Scattered Light Time-history Diagnostic (SLTD) is being implemented at the National Ignition Facility (NIF) to greatly expand the angular coverage of absolute scattered-light measurements for direct- and indirect-drive inertial confinement fusion (ICF) experiments. The SLTD array will ultimately consist of 15 units mounted at a variety of polar and azimuthal angles on the NIF target chamber, complementing the existing NIF backscatter suite. Each SLTD unit collects and diffuses scattered light onto a set of three optical fibers, which transport the light to filtered photodiodes to measure scattered light in different wavelength bands: stimulated Brillouin scattering (350 nm-352 nm), stimulated Raman scattering (430 nm-760 nm), and ω/2 (695 nm-745 nm). SLTD measures scattered light with a time resolution of ∼1 ns and a signal-to-noise ratio of up to 500. Currently, six units are operational and recording data. Measurements of the angular dependence of scattered light will strongly constrain models of laser energy coupling in ICF experiments and allow for a more robust inference of the total laser energy coupled to implosions.

Conformation of the O-specific polysaccharide of Shigella dysenteriae type 1: molecular modeling shows a helical structure with efficient exposure of the antigenic determinant alpha-L-Rhap-(1-->2)-alpha-D-Galp.

The O-specific polysaccharide of Shigella dysenteriae type 1, which has the repeating tetrasaccharide unit -->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->2)-alpha-D-Galp-(1-->3)-alpha-D-GlcNAcp-(1--> (A-B-C-D), is a major virulence factor, and it is believed that antibodies against this polysaccharide confer protection to the host. The conformational properties of fragments of this O-antigen were explored using systematic search with a modified HSEA method (GLYCAN) and with molecular mechanics MM3(96). The results show that the alpha-D-Gal-(1-->3)-alpha-D-GlcNAc linkage adopts two favored conformations, phi/psi approximately equal to -40 degrees /-30 degrees (I) and approximately 15 degrees /30 degrees (II), whereas the other glycosidic linkages only have a single favored phi/psi conformational range. MM3 indicates that the trisaccharide B-C-D and tetrasaccharides containing the B-C-D moiety exist as two different conformers, distinguished by the conformations I and II of the C-D linkage. For the pentasaccharide A-B-C-D-A' and longer fragments, the calculations show preference for the C-D conformation II. These results can explain previously reported nuclear magnetic resonance data. The pentasaccharide in its favored conformation II is sharply bent, with the galactose residue exposed at the vertex. This hairpin conformation of the pentasaccharide was successfully docked with the binding site of a monoclonal IgM antibody (E3707 E9) that had been homology modeled from known crystal structures. For fragments made of repetitive tetrasaccharide units, the hairpin conformation leads to a left-handed helical structure with the galactose residues protruding radially at the helix surface. This arrangement results in a pronounced exposure of the galactose and also the adjacent rhamnose in each repeating unit, which is consistent with the known role of the as alpha-L-Rhap-(1-->2)-alpha-D-Galp moiety as a major antigenic epitope of this O-specific polysaccharide.

Characterization of the interaction of Ca2+ with hydroxy and non-hydroxy fatty acid species of cerebroside sulfate by Fourier transform infrared spectroscopy and molecular modeling.

Ca2+-mediated interactions between the carbohydrate groups of glycolipids, including that of cerebroside sulfate (galactosylceramide I3-sulfate), have recently been implicated as a basis of cell recognition and adhesion. Hydroxylation of the fatty acid of this lipid has an effect on these interactions. Therefore, FT-IR spectroscopy was used to study the interaction of Ca2+ with semisynthetic hydroxy (HFA) and non-hydroxy fatty acid (NFA) species of cerebroside sulfate (CBS). Ca2+ caused partial dehydration of the sulfate group and reduced hydrogen bonding of the sugar hydroxyls of both species. The amide I and II bands of the lipids in the absence of Ca2+ (NH4+ salt forms) suggested that the N-H of the HFA species is involved in a bent intramolecular hydrogen bond, probably with the fatty acid hydroxyl group and the glycosidic oxygen, while that of the NFA species is involved in a linear intermolecular hydrogen bond with the C=O and/or other oxygens. Ca2+ caused a rearrangement of the hydrogen-bonding network in the interfacial region of the HFA species involving the amide group. The results suggested increased hydrogen bonding of the C=O and a shift in hydrogen bonding of the N-H of the Ca2+ salt form of the HFA species from a bent intramolecular hydrogen bond to a linear intermolecular hydrogen bond, probably with the C=O of neighboring molecules, similar to the NFA species. The involvement of the fatty acid alpha-hydroxyl group in the rearranged network was indicated by a reduction in mobility of the alpha-CH group of the HFA species, in contrast to that of the NFA species. Participation of the alpha-OH group in hydrogen-bonding networks in the interfacial region of both the NH4+ and Ca2+ salt forms caused a significant increase in the interchain packing, as evident from correlation field splitting of the HFA-CBS methylene scissoring mode, while this did not occur for the NFA species. The absence of intramolecular hydrogen bonding of the N-H with the glycosidic oxygen for both salt forms of the NFA species and for the Ca2+ salt form of the HFA species may destabilize the "bent shovel", bilayer planar conformation of the sugar and cause it to be in the extended, bilayer perpendicular conformation. Calculations of the three-dimensional interaction energy of Ca2+ with CBS showed strong binding around the sulfate and the surface of galactose facing the bilayer in the bent shovel conformation. Ca2+ binding at this surface would disrupt intra- and intermolecular hydrogen-bonding interactions of the head group, thus accounting for its effect in inducing a transition to the extended conformation.

NMR study of the conformation of galactocerebroside in bilayers and solution: galactose reorientation during the metastable-stable gel transition.

Conformations of two types of bovine brain cerebroside containing normal and alpha-hydroxy-fatty acids (NFA-CER and HFA-CER, respectively) in solution and in bilayers were investigated using 1H and 13C NMR in solution and in the solid state. The analysis of vicinal 1H-1H coupling constants and NOE measurements in solution indicated that in both cerebrosides the predominant conformation about the O1-C1, C1-C2, and C2-C3 bonds is ap/-sc/ap, respectively. The remarkable similarity in the 13C NMR chemical shifts in solution and in hydrated liquid-crystalline bilayers indicated that both cerebrosides in bilayers assume conformation essentially identical to those in solution. The obtained 13C NMR spectra in solution were used as a reference for comparison with the variable-temperature 13C CP-MAS NMR spectra in the metastable and stable gel phases. The lack of chemical shift changes of polar carbon atoms upon cooling the HFA-CER bilayers below the Tm strongly suggests that the liquid-crystalline-metastable gel transition is not associated with a conformational change of the head group. The observed line broadening can be interpreted in terms of the hydrocarbon chain crystallization and slow dynamics of the head group in the metastable phase. On the other hand, the relaxation of the metastable gel phase of HFA-CER caused profound changes in the 13C spectra, primarily of the signals of the galactose C1, the ceramide C2, C4, and C5, and the carbonyl group. These changes are interpreted using the known dependence of the chemical shifts of anomeric carbon on the conformation about the O1-C1 bond to suggest that the gel phase relaxation involves a significant reorientation of the galactose moiety caused by a change in the rotation of the O1-C1 bond from the ap to -sc conformer. Similar changes of chemical shifts were observed in the case of NFA-CER during the transition from the liquid-crystalline phase to the stable gel phase.

Two distinct binding sites for globotriaosyl ceramide on verotoxins: identification by molecular modelling and confirmation using deoxy analogues and a new glycolipid receptor for all verotoxins.

BACKGROUND: The Escherichia coli verotoxins (VTs) can initiate human vascular disease via the specific recognition of globotriaosyl-ceramide (Gb3) on target endothelial cells. To explore the structural basis for receptor recognition by different VTs we used molecular modelling based on the crystal structure of VT1, mutational data and binding data for deoxy galabiosyl receptors. RESULTS: We propose a model for the verotoxin 'cleft-site complex' with Gb3. Energy minimizations of Gb3 within the 'cleft site' of verotoxins VT1, VT2, VT2c and VT2e resulted in stable complexes with hydrogen-bonding systems that were in agreement with binding data obtained for mono-deoxy analogues of Gb3. N-deacetylated globoside (aminoGb4), which was found to be a new, efficient receptor for all verotoxins, can be favourably accommodated in the cleft site of the VTs by formation of a salt bridge between the galactosamine and a cluster of aspartates in the site. The model is further extended to explain the binding of globoside by VT2e. Docking data support the possibility of an additional binding site for Gb3 on VT1. CONCLUSIONS: The proposed models for the complexes of verotoxins with their globoglycolipid receptors are consistent with receptor analogue binding data and explain previously published mutational studies. The results provide a first approach to the design of specific inhibitors of VT-receptor binding.

Modelling of the interaction of verotoxin-1 (VT1) with its glycolipid receptor, globotriaosylceramide (Gb3).

Possible binding sites for the glycolipid globotriaosylceramide (Gal alpha 1-->4Gal beta 1-->4Glc beta 1-->1 Cer; Gb3) on the B-subunits of verotoxin-1 (VT1) were explored using binding data for specifically mutated verotoxins and by computational docking of favoured conformers of Gb3 with the crystal structure of VT1. Calculations using the GRID program suggested a site with favourable hydrophobic interactions at the exposed side chain of Phe30. One of the favoured conformers of Gb3 was docked into this site, with the hydrophobic face of the internal Gal beta residue in contact with the side chain of Phe30. After energy minimization, the two terminal saccharide residues of Gb3 (Gal alpha and Gal beta) showed favourable interactions with the toxin. In the proposed model of the complex, the terminal Gal alpha of Gb3 is located in proximity to aspartates 16-18 of VT1. The model is in agreement with available experimental binding data for the interaction of globoglycolipids with different naturally occurring and mutated verotoxins.

Steric presentation and recognition of the saccharide chains of glycolipids at the cell surface: favoured conformations of the saccharide-lipid linkage calculated using molecular mechanics (MM3).

The orientation of the saccharide moiety of glycolipids at the membrane surface is determined by an interplay of different steric factors, e.g. the conformation of the saccharide chain, the conformation of the saccharide-lipid linkage and restrictions due to the membrane surface. In the present study the preferred conformations of the saccharide-lipid linkages of glucosylceramides with normal and hydroxy fatty acids and glucosyldiglycerides with acyl and alkyl chains were studied using molecular mechanics (MM3). The populations of different conformers were calculated on the basis of relaxed energy maps. Calculations on glucosylceramides at a dielectric constant (epsilon) of 4 showed three dominating conformers: phi/psi/theta 1 = +sc/ap/-sc (global energy minimum), /-sc/ap and +sc/ap/ap, respectively. In sphingolipids the +sc rotamer of theta 1 is disfavoured due to a Hassel-Ottar interaction involving the sphingosine O1 and O3 oxygen atoms. alpha-O Hydroxylation of the fatty acid does not significantly affect the conformational preferences of the saccharide-ceramide linkage at epsilon-values relevant for biomembranes. In glycoglycerolipids the global energy minimum is shifted to the phi/psi/theta 1 = +sc/ap/ap conformation. For glycolipids located in membranes additional steric restrictions are imposed by the surrounding lipid layer. These restrictions in the steric presentation appear to be of crucial significance for the selective recognition and crypticity of glycolipids in membranes.

Orientation of the saccharide chains of glycolipids at the membrane surface: conformational analysis of the glucose-ceramide and the glucose-glyceride linkages using molecular mechanics (MM3).

Preferred conformations of the saccharide-ceramide linkage of glucosylceramides with different ceramide structures (normal and hydroxy fatty acids) were investigated by molecular mechanics (MM3) calculations and compared with conformational features obtained for glucosylglycerolipids (diacyl and dialkyl analogues). Relaxed energy map calculations with MM3 were performed for the three bonds (C1'-O1-C1-C2, torsion angles phi, psi, and theta 1) of the glucose-ceramide/diglyceride linkage at different values of the dielectric constant. For the phi torsion of the glycosidic C1'-O1 bond the calculations show a strict preference for the +sc range whereas the psi/theta 1 energy surface is dependent on the structure of the lipid moiety as well as on the dielectric constant (epsilon). Calculations performed on glucosylceramide with normal and hydroxy fatty acids at epsilon = 4 (bilayer subsurface conditions) show three dominating conformers (psi/theta 1 = ap/-sc, -sc/ap, and ap/ap). The ap/-sc conformer, which represents the global energy minimum, is stabilized by polar interactions involving the amide group. The +sc rotamer of theta 1 is unfavored in sphingolipids due to a Hassel-Ottar effect involving the sphingosine O3 and O1 oxygen atoms. Comparative calculations on glycosylglycerolipid analogues (ester and ether derivatives) show a distinct preference for the ap rotamer of theta 1. An evaluation of the steric hindrance imposed by the surrounding membrane surface shows that in a bilayer arrangement the range of possible conformations for the saccharide-lipid linkage is considerably reduced. The significance of preferred conformations of the saccharide-ceramide linkage for the presentation and recognition of the saccharide chains of glycosphingolipids at the membrane surface is discussed.

Serological and immunochemical characterization of anti-PP1Pk (anti-Tja) antibodies in blood group little p individuals. Blood group A type 4 recognition due to internal binding.

Serum samples from 13 blood group little p individuals were tested by radioimmunoassay for their IgG antibody subclass distribution against the P, P1 and Pk antigens. There was no uniform subclass distribution pattern, although all but one had IgG3 antibodies against all the P system antigens tested. Studies were performed adsorbing anti-Tja serum sequentially to columns with synthetic carbohydrate antigenic determinants within the P system coupled to silica beads (SynsorbsR). The effect on agglutinin and indirect antiglobulin titers was determined after adsorption to SynsorbsR with different P-system antigens (P1, Pk, P). Adsorption to all the three SynsorbsR was needed to eliminate or strongly reduce antibody titers. The effect on IgM, IgG, IgA as well as IgG subclass antibody binding to P, P1 and Pk antigens was also determined by radioimmunoassay and chromatogram binding assay. Anti-PP1Pk antibodies from a little p woman with repeated abortions were shown to bind to glycosphingolipid antigens prepared from one of the aborted placentae using a chromatogram binding assay. This binding was eliminated by serum adsorption to SynsorbsR with P1, Pk and P carbohydrates. Anti-PP1Pk antibodies were also shown to bind to extended structures in the globoseries, i.e. globopentaosylceramide, globohexaosylceramide (globo-H) and globoheptaosylceramide (globo-A). This binding is most probably due to antibodies recognizing internal sequences in the carbohydrate chain. Attempts were made to visualize the binding epitope of the antibodies by computer molecular modelling.

Characterisation of the anti-A antibody response following an ABO incompatible (A2 to O) kidney transplantation.

Anti-A,B antibodies produced in a blood group OLe(a-b-) recipient receiving a kidney graft from a blood group A2Le(a-b+) donor have been analysed for their ability to bind to different glycosphingolipid antigens. Solid-phase RIA using pure glycosphingolipid antigens and a chromatogram binding assay using total nonacid glycosphingolipid fractions from erythrocytes of different human blood group phenotypes together with pure glycolipid antigens were used as assay systems. Serum antibodies were shown to bind equally well to A (types 1, 2, 3 and 4) and B (types 1 and 2) antigenic structures but no binding to H antigens (types 1, 2 and 4) was detected. After adsorption of serum antibodies on A1 Le(a-b+) erythrocytes there was a residual anti-A antibody activity which could not be adsorbed by synthetic A-trisaccharides coupled to crystalline silica (Synsorb-A). These residual antibodies, which are not present in a pretransplant serum sample, had a specificity for the A antigen with type 1 core saccharide chain and the binding epitope obviously included both the N-acetylgalactosamine and the N-acetylglucosamine. The fucose residue was apparently not obligate for binding. The conformation of the sugar units involved in the binding epitope was determined.

Saccharide orientation at the cell surface affects glycolipid receptor function.

Three allelic variants of P-pilus-associated G-adhesins (lectins) with different cell-binding properties were recently described. Here we have analyzed Escherichia coli HB101 strains expressing the recombinant G-adhesin variants for their ability to agglutinate erythrocytes from various species as this relates to the glycosphingolipid (GSL) composition in the erythrocyte membranes. All three variants exhibit similar specificities for the globo-series GSLs affixed to artificial surfaces. However, only the PapGJ96 adhesin induces agglutination of erythrocytes having globotriaosylceramide (GbO3) [Gal(alpha 1-4)LacCer] as the major GSL. Furthermore, only PapGAD110 induces strong agglutination of erythrocytes having globotetraosylceramide (GbO4) [GalNAc(beta 1-3)Gal(alpha 1-4)LacCer] as the major GSL, while PrsGJ96 alone agglutinates those containing globopentaosylceramide (GbO5) [GalNAc(alpha 1-3)GalNAc(beta 1-3)Gal(alpha 1-4)LacCer]. Molecular modeling of these globo-GSLs demonstrates different saccharide orientations to the membrane surface for these isoreceptors. We suggest that the differential binding of the three G-adhesin variants results from differences in epitope presentation at the membrane among these globo-GSLs.

The effect of hydrogen bonds on the conformation of glycosphingolipids. Methylated and unmethylated cerebroside studied by X-ray single crystal analysis and model calculations.

The conformation and molecular packing of permethylated beta-D-galactosyl-N-octadecanoyl-D-spingosine (cerebroside) was determined by X-ray single crystal analysis at 185 K (R = 0.16). The lipid crystallizes in the orthorhombic space group P2(1)2(1)2(1) with the unit cell dimensions a = 8.03, b = 7.04 and c = 88.10 A. The four molecules in the unit cell pack in a bilayer arrangement with tilting (48 degrees) hydrocarbon chains. The direction of the chain tilt alternates in the two bilayer halves and in adjacent bilayers. In order to define the effect of hydrogen bonds on the molecular conformation the structural features of the permethylated cerebroside are compared with that of unsubstituted cerebroside (I. Pascher and S. Sundell (1977) Chem. Phys. Lipids 20, 179). It is shown that methylation of the hydrogen donor groups does not affect the conformation of the ceramide part. However, by abolishing the intramolecular hydrogen bond between the amide N--H group and the glycosidic oxygen the galactose ring changes its orientation from layer-parallel to layer-perpendicular. Calculations using molecular mechanics, MM2(87), show that in natural cerebroside the intramolecular hydrogen bond stabilizes the theta 1 = -syn-clinal conformation about the C(1)--C(2) sphingosine bond by 2-2.5 kcal/mol compared to other staggered conformations. The significance of the L shape of the native cerebroside, making both the carbohydrate and polar ceramide groups accessible as a binding epitope in recognition processes, is discussed.

Conformational analysis of blood group A-active glycosphingolipids using HSEA-calculations. The possible significance of the core oligosaccharide chain for the presentation and recognition of the A-determinant.

Conformational analysis of four different A-active glycosphingolipids, A types 1-4, was carried out using HSEA-calculations with the GESA-program. In their minimum energy conformations the oligosaccharide chains are more or less curved; in particular the type 3 and 4 have a strongly bent shape. When the carbohydrate structures are linked to ceramide, using the conformational features predominantly observed in crystal structures of membrane lipids, rather drastic differences in the orientation of the oligosaccharide chains are obtained. For the type 1 glycosphingolipid the model study indicates that the A-determinant extends almost perpendicularly to the membrane plane whereas for type 2, 3 and 4 the terminal part of the oligosaccharide chains is more parallel to the membrane. The fucose branch on type 3 and type 4 thereby appears directed towards the environment whereas for type 2 it would face the membrane. Due to restrictions imposed by the membrane layer this core specific orientation is largely preserved even if the flexibility of the saccharide-ceramide linkage is taken into account. Hydrophilic and hydrophobic sites on the surface of the different oligosaccharide chains in their minimum energy conformation were located using the GRID-program. It is suggested that the core-dependent presentation of the A-determinant might explain the chain type specificity observed for different monoclonal anti-A antibodies. The results further suggest that assay systems ensuring a membrane-like presentation of the glycolipid antigen should be used in studies of glycolipid/protein interactions.

On the dissection of binding epitopes on carbohydrate receptors for microbes using molecular modelling.

The most common receptors for microbes on animal cells seem to be carbohydrates. One characteristic property of microbial protein-carbohydrate interaction is the recognition of sequences placed within an oligosaccharide chain. This leads to a series of isoreceptors defined as saccharides carrying the particular receptor sequence with different neighbouring groups. A microbial ligand may have different binding affinities for such isoreceptors depending upon steric hindrance from neighbouring groups upon access to the binding epitope. By a comparison of binding preferences to a series of isoreceptors with their calculated conformation, the binding epitope on a particular receptor sequence may be approximated by use of molecular modelling. This approach is illustrated for two bacteria recognising lactosylceramide. The potential importance of the procedure for further developments including drug design is briefly discussed.