NMR methods for characterizing the pore structures and hydrogen storage properties of microporous carbons.

(1)H NMR spectroscopy is used to investigate a series of microporous activated carbons derived from a poly(ether ether ketone) (PEEK) precursor with varying amounts of burnoff (BO). In particular, properties relevant to hydrogen storage are evaluated such as pore structure, average pore size, uptake, and binding energy. High-pressure NMR with in situ H(2) loading is employed with H(2) pressure ranging from 100 Pa to 10 MPa. An N(2)-cooled cryostat allows for NMR isotherm measurements at both room temperature ( approximately 290 K) and 100 K. Two distinct (1)H NMR peaks appear in the spectra which represent the gaseous H(2) in intergranular pores and the H(2) residing in micropores. The chemical shift of the micropore peak is observed to evolve with changing pressure, the magnitude of this effect being correlated to the amount of BO and therefore the structure. This is attributed to the different pressure dependence of the amount of adsorbed and non-adsorbed molecules within micropores, which experience significantly different chemical shifts due to the strong distance dependence of the ring current effect. In pores with a critical diameter of 1.2 nm or less, no pressure dependence is observed because they are not wide enough to host non-adsorbed molecules; this is the case for samples with less than 35% BO. The largest estimated pore size that can contribute to the micropore peak is estimated to be around 2.4 nm. The total H(2) uptake associated with pores of this size or smaller is evaluated via a calibration of the isotherms, with the highest amount being observed at 59% BO. Two binding energies are present in the micropores, with the lower, more dominant one being on the order of 5 kJ mol(-1) and the higher one ranging from 7 to 9 kJ mol(-1).

High number of antigen binding cells in unimmunized mice and possible occurrence of multispecific lymphocytes

A high frequency of Tobacco Mosaic virus (TMV) binding cells was found in spleen cells from unimmunized mice (about 3 to 4%). TMV binding is strongly inhibited by previous incubation with anti immunoglobulin antisera. After stripping of membrane receptors, a full recovery for antigen binding capacity can be observed after 24 hr culture. Experiments are presented to exclude artefactual fluorescent cells: interaction of TMV with some non immunoglobulin membrane components; interaction of fluorescent anti TMV antibody with the Fc receptor of B cells; the binding of TMV to cytophilic immunoglobulins. The occurrence of lymphocytes able to bind several non crossreactive antigens is suggested by three lines of evidence: the high number of antigen binding cells in unimmunized mice, presence of surface immunoglobulins on some TMV binding cells after complete capping of TMV receptors and the direct demonstration of lymphocytes binding TMV and hemocyanin at different membrane sites.

Regulation of the alpha-fetoprotein promoter: Ku binding and DNA spatial conformation

This work shows that the proximal promoter of the mouse Afp gene contains a Ku binding site and that Ku binding is associated with down-regulation of the transcriptional activity of the Afp promoter. The Ku binding site is located in a segment able to adopt a peculiar structured form, probably a hairpin structure. Interestingly, the structured form eliminates the binding sites of the positive transcription factor HNF1. Furthermore, a DNAse hypersensitive site is detected in footprinting experiments done with extracts of AFP non-expressing hepatoma cells. These observations suggest that the structured form is stabilised by Ku and is associated with extinction of the gene in AFP non-expressing hepatic cells.

The Physical and Chemical Structure of Hot Molecular Cores

We have made self-consistent models of the density and temperature profiles of the gas and dust surrounding embedded luminous objects using a detailed radiative transfer model together with observations of the spectral energy distribution of hot molecular cores. Using these profiles we have investigated the hot core chemistry which results when grain mantles are evaporated, taking into account the different binding energies of the mantle molecules, as well a model in which we assume that all molecules are embedded in water ice and have a common binding energy. We find that most of the resulting column densities are consistent with those observed toward the hot core G34.3+0.15 at a time around 10^4 years after central luminous star formation. We have also investigated the dependence of the chemical structure on the density profile which suggests an observational possibility of constraining density profiles from determination of the source sizes of line emission from desorbed molecules.

Relevance of heterometallic binding energy for metal underpotential deposition

We present first-principles calculations for a number of metals adsorbed on several different metallic substrates. Some of these systems are very relevant in electrochemistry, especially in the field of underpotential deposition phenomena. The present studies reveal the existence of a relationship between the excess binding energy and the surface energy difference between substrate and adsorbate. Comparisons with experimental underpotential shifts show that excess binding energies are systematically underestimated. By analyzing experimental information on different systems, we conclude that this discrepancy between our vacuum calculations and experiments carried out in an electrolytic solution is likely to be due to anion adsorption and/or solvent effects.

Degradation, receptor binding, insulin secreting and antihyperglycaemic actions of palmitate-derivatised native and Ala(8)-substituted GLP-1 analogues

The hormone glucagonlike peptide-1(736)amide (GLP-1) is released in response to ingested nutrients and acts to promote glucosedependent insulin secretion ensuring efficient postprandial glucose homeostasis. Unfortunately, the beneficial actions of GLP-1 which give this hormone many of the desirable properties of an antidiabetic drug are short lived due to degradation by dipeptidylpeptidase IV (DPP IV) and rapid clearance by renal filtration. In this study we have attempted to extend GLP-1 action through the attachment of palmitoyl moieties to the epsilon-amino group in the side chain of the Lys(26) residue and to combine this modification with substitutions of the Ala(8) residue, namely Val or aminobutyric acid (Abu). In contrast to native GLP-1, which was rapidly degraded, [Lys(pal)(26)]GLP-1, [Abu(8),Lys(pal)(26)]GLP-1 and [Val(8),Lys(pal)(26)]GLP-1 all exhibited profound stability during 12 h incubations with DPP IV and human plasma. Receptor binding affinity and the ability to increase cyclic AMP in the clonal beta-cell line BRIN-BD11 were decreased by 86- to 167-fold and 15- to 62-fold, respectively compared with native GLP-1. However, insulin secretory potency tested using BRIN-BD11 cells was similar, or in the case of [Val(8),Lys(pal)(26)]GLP-1 enhanced. Furthermore, when administered in vivo together with glucose to diabetic (ob/ob) mice, [Lys(pal)(26)]GLP-1, [Abu(8),Lys(pal)(26)]GLP-1 and [Val8,Lys(pal)26]GLP-1 did not demonstrate acute glucoselowering or insulinotropic activity as observed with native GLP-1. These studies support the potential usefulness of fatty acid linked analogues of GLP-1 but indicate the importance of chain length for peptide kinetics and bioavailability.

Positron-molecule interactions: Resonant attachment, annihilation, and bound states

This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment, and annihilation. Measurements of annihilation rates resolved as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFRs) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecule (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. Molecules that do not bind positrons and hence do not exhibit such resonances are discussed. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom, approximately as the fourth power of the number of atoms in the molecule. While the details are as yet unclear, intramolecular vibrational energy redistributio (IVR) to states that do not couple directly to the positron continuum appears to be responsible for these enhanced annihilation rates. In connection with IVR, experimental evidence indicates that inelastic positron escape channels are relatively rare. Downshifts of the VFR from the vibrational mode energies, obtained by measuring annihilate rates as a function of incident positron energy, have provided binding energies for 30 species. Their dependence upon molecular parameters and their relationship to positron-atom and positron-molecule binding-energy calculations are discussed. Feshbach resonances and positron binding to molecules are compared with the analogous electron-molecul (negative-ion) cases. The relationship of VFR-mediated annihilation to other phenomena such as Doppler broadening of the gamma-ray annihilation spectra, annihilation of thermalized positrons in gases, and annihilation-induced fragmentation of molecules is discussed. Possible areas for future theoretical and experimental investigation are also discussed.

Many-body theory calculations of positron binding to negative ions

A many-body theory approach developed by the authors [Phys. Rev. A 70, 032720 (2004)] is applied to positron bound states and annihilation rates in atomic systems. Within the formalism, full account of virtual positronium (Ps) formation is made by summing the electron-positron ladder diagram series, thus enabling the theory to include all important many-body correlation effects in the positron problem. Numerical calculations have been performed for positron bound states with the hydrogen and halogen negative ions, also known as Ps hydride and Ps halides. The Ps binding energies of 1.118, 2.718, 2.245, 1.873 and 1.393 eV and annihilation rates of 2.544, 2.482, 1.984, 1.913 and 1.809 ns^{-1}, have been obtained for PsH, PsF, PsCl, PsBr and PsI, respectively.

Comparison of the binding specificity of two bacterial metalloproteases, LasB of Pseudomonas aeruginosa and ZapA of Proteus mirabilis, using N-alpha mercaptoamide template-based inhibitor analogues

The metalloproteases ZapA of Proteus mirabilis and LasB of Pseudomonas aeruginosa are known to be virulence factors their respective opportunistic bacterial pathogens, and are members of the structurally related serralysin and thermolysin families of bacterial metalloproteases respectively. Secreted at the site of infection, these proteases play a key role in the infection process, contributing to tissue destruction and processing of components of the host immune system. Inhibition of these virulence factors may therefore represent an antimicrobial strategy, attenuating the virulence of the infecting pathogen. Previously we have screened a library of N-alpha mercaptoamide dipeptide inhibitors against both ZapA and LasB, with the aim of mapping the S1' binding site of the enzymes, revealing both striking similarities and important differences in their binding preferences. Here we report the design, synthesis, and screening of several inhibitor analogues, based on two parent inhibitors from the original library. The results have allowed for further characterization of the ZapA and LasB active site binding pockets, and have highlighted the possibility for development of broad-spectrum bacterial protease inhibitors, effective against enzymes of the thermolysin and serralysin metalloprotease families.

P2Y(1) antagonists: Combining receptor-based modeling and QSAR for a quantitative prediction of the biological activity based on consensus scoring

P2Y(1) is an ADP-activated G protein-coupled receptor (GPCR). Its antagonists impede platelet aggregation in vivo and are potential antithrombotic agents. Combining ligand and structure-based modeling we generated a consensus model (LIST-CM) correlating antagonist structures with their potencies. We docked 45 antagonists into our rhodopsin-based human P2Y(1) homology model and calculated docking scores and free binding energies with the Linear Interaction Energy (LIE) method in continuum-solvent. The resulting alignment was also used to build QSAR based on CoMFA, CoMSIA, and molecular descriptors. To benefit from the strength of each technique and compensate for their limitations, we generated our LIST-CM with a PLS regression based on the predictions of each methodology. A test set featuring untested substituents was synthesized and assayed in inhibition of 2-MeSADP-stimulated PLC activity and in radioligand binding. LIST-CM outperformed internal and external predictivity of any individual model to predict accurately the potency of 75% of the test set.

Positron scattering and annihilation in hydrogenlike ions

Diagrammatic many-body theory is used to calculate the scattering phase shifts, normalized annihilation rates Zeff, and annihilation ? spectra for positron collisions with the hydrogenlike ions He+, Li2+, B4+, and F8+. Short-range electron-positron correlations and longer-range positron-ion correlations are accounted for by evaluating nonlocal corrections to the annihilation vertex and the exact positron self-energy. The numerical calculation of the many-body theory diagrams is performed using B-spline basis sets. To elucidate the role of the positron-ion repulsion, the annihilation rate is also estimated analytically in the Coulomb-Born approximation. It is found that the energy dependence and magnitude of Zeff are governed by the Gamow factor that characterizes the suppression of the positron wave function near the ion. For all of the H-like ions, the correlation enhancement of the annihilation rate is found to be predominantly due to corrections to the annihilation vertex, while the corrections to the positron wave function play only a minor role. Results of the calculations for s-, p-, and d-wave incident positrons of energies up to the positronium-formation threshold are presented. Where comparison is possible, our values are in excellent agreement with the results obtained using other, e.g., variational, methods. The annihilation-vertex enhancement factors obtained in the present calculations are found to scale approximately as 1+(1.6+0.46l)/Zi, where Zi is the net charge of the ion and l is the positron orbital angular momentum. Our results for positron annihilation in H-like ions provide insights into the problem of positron annihilation with core electrons in atoms and condensed matter systems, which have similar binding energies.

Comparative biochemical analysis of three members of the Schistosoma mansoni TAL family: Differences in ion and drug binding properties

The tegumental allergen-like (TAL) proteins from Schistosoma mansoni are part of a family of calcium binding proteins found only in parasitic flatworms. These proteins have attracted interest as potential drug or vaccine targets, yet comparatively little is known about their biochemistry. Here, we compared the biochemical properties of three members of this family: SmTAL1 (Sm22.6), SmTAL2 (Sm21.7) and SmTAL3 (Sm20.8). Molecular modelling suggested that, despite similarities in domain organisation, there are differences in the three proteins’ structures. SmTAL1 was predicted to have two functional calcium binding sites and SmTAL2 was predicted to have one. Despite the presence of two EF-hand-like structures in SmTAL3, neither was predicted to be functional. These predictions were confirmed by native gel electrophoresis, intrinsic fluorescence and differential scanning fluorimetry: both SmTAL1 and SmTAL2 are able to bind calcium ions reversibly, but SmTAL3 is not. SmTAL1 is also able to interact with manganese, strontium, iron(II) and nickel ions. SmTAL2 has a different ion binding profile interacting with cadmium, manganese, magnesium, strontium and barium ions in addition to calcium. All three proteins form dimers and, in contrast to some Fasciola hepatica proteins from the same family; dimerization is not affected by calcium ions. SmTAL1 interacts with the anti-schistosomal drug praziquantel and the calmodulin antagonists trifluoperazine, chlorpromazine and W7. SmTAL2 interacts only with W7. SmTAL3 interacts with the aforementioned calmodulin antagonists and thiamylal, but not praziquantel. Overall, these data suggest that the proteins have different biochemical properties and thus, most likely, different in vivo functions.

Free fatty acid receptors:structural models and elucidation of ligand binding interactions

BACKGROUND: The free fatty acid receptors (FFAs), including FFA1 (orphan name: GPR40), FFA2 (GPR43) and FFA3 (GPR41) are G protein-coupled receptors (GPCRs) involved in energy and metabolic homeostasis. Understanding the structural basis of ligand binding at FFAs is an essential step toward designing potent and selective small molecule modulators.

RESULTS: We analyse earlier homology models of FFAs in light of the newly published FFA1 crystal structure co-crystallized with TAK-875, an ago-allosteric ligand, focusing on the architecture of the extracellular binding cavity and agonist-receptor interactions. The previous low-resolution homology models of FFAs were helpful in highlighting the location of the ligand binding site and the key residues for ligand anchoring. However, homology models were not accurate in establishing the nature of all ligand-receptor contacts and the precise ligand-binding mode. From analysis of structural models and mutagenesis, it appears that the position of helices 3, 4 and 5 is crucial in ligand docking. The FFA1-based homology models of FFA2 and FFA3 were constructed and used to compare the FFA subtypes. From docking studies we propose an alternative binding mode for orthosteric agonists at FFA1 and FFA2, involving the interhelical space between helices 4 and 5. This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42. The novel FFAs structural models highlight higher aromaticity of the FFA2 binding cavity and higher hydrophilicity of the FFA3 binding cavity. The role of the residues at the second extracellular loop used in mutagenesis is reanalysed. The third positively-charged residue in the binding cavity of FFAs, located in helix 2, is identified and predicted to coordinate allosteric modulators.

CONCLUSIONS: The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions. Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

A comparative study of Type II-P and II-L supernova rise times as exemplified by the case of LSQ13cuw

We report on our findings based on the analysis of observations of the Type II-L supernova LSQ13cuw within the framework of currently accepted physical predictions of core-collapse supernova explosions. LSQ13cuw was discovered within a day of explosion, hitherto unprecedented for Type II-L supernovae. This motivated a comparative study of Type II-P and II-L supernovae with relatively well-constrained explosion epochs and rise times to maximum (optical) light. From our sample of twenty such events, we find evidence of a positive correlation between the duration of the rise and the peak brightness. On average, SNe II-L tend to have brighter peak magnitudes and longer rise times than SNe II-P. However, this difference is clearest only at the extreme ends of the rise time versus peak brightness relation. Using two different analytical models, we performed a parameter study to investigate the physical parameters that control the rise time behaviour. In general, the models qualitatively reproduce aspects of the observed trends. We find that the brightness of the optical peak increases for larger progenitor radii and explosion energies, and decreases for larger masses. The dependence of the rise time on mass and explosion energy is smaller than the dependence on the progenitor radius. We find no evidence that the progenitors of SNe II-L have significantly smaller radii than those of SNe II-P.

Novel Prostate Specific Antigen plastic antibody designed withcharged binding sites for an improved protein binding and itsapplication in a biosensor of potentiometric transduction

This work shows that the synthesis of protein plastic antibodies tailored with selected charged monomersaround the binding site enhances protein binding. These charged receptor sites are placed over a neutralpolymeric matrix, thus inducing a suitable orientation the protein reception to its site. This is confirmed bypreparing control materials with neutral monomers and also with non-imprinted template. This concepthas been applied here to Prostate Specific Antigen (PSA), the protein of choice for screening prostate can-cer throughout the population, with serum levels >10 ng/mL pointing out a high probability of associatedcancer.Protein Imprinted Materials with charged binding sites (C/PIM) have been produced by surfaceimprinting over graphene layers to which the protein was first covalently attached. Vinylben-zyl(trimethylammonium chloride) and vinyl benzoate were introduced as charged monomers labellingthe binding site and were allowed to self-organize around the protein. The subsequent polymerizationwas made by radical polymerization of vinylbenzene. Neutral PIM (N/PIM) prepared without orientedcharges and non imprinted materials (NIM) obtained without template were used as controls.These materials were used to develop simple and inexpensive potentiometric sensor for PSA. Theywere included as ionophores in plasticized PVC membranes, and tested over electrodes of solid or liq-uid conductive contacts, made of conductive carbon over a syringe or of inner reference solution overmicropipette tips. The electrodes with charged monomers showed a more stable and sensitive response,with an average slope of -44.2 mV/decade and a detection limit of 5.8 × 10−11mol/L (2 ng/mL). The cor-responding non-imprinted sensors showed lower sensitivity, with average slopes of -24.8 mV/decade.The best sensors were successfully applied to the analysis of serum, with recoveries ranging from 96.9to 106.1% and relative errors of 6.8%.