Crystal structure of Escherichia coli xanthine phosphoribosyltransferase

Xanthine phosphoribosyltransferase (XPRT; EC 2.4.2.22) from Escherichia coil is a tetrameric enzyme having 152 residues per subunit. XPRT catalyzes the transfer of the phosphoribosyl group from 5-phospho-alpha-D-ribosyl l-pyrophosphate (PRib-PP) to the 6-oxopurine bases guanine, xanthine, and hypoxanthine to form GMP, XMP, and IMP, respectively. Crystals grown in the absence of substrate or product were used to determine the structure of XPRT at a resolution of 1.8 Angstrom by multiple isomorphous replacement. The core structure of XPRT includes a five-stranded parallel B-sheet surrounded by three or-helices, which is similar to that observed in other known phosphoribosyltransferase (PRTase) structures. The XPRT structure also has several interesting features. A glutamine residue in the purine binding site may be responsible for the altered 6-oxopurine base specificity seen in this enzyme compared to other 6-oxopurine PRTases. Also, we observe both a magnesium ion and a sulfate ion bound at the PRib-PP binding site of XPRT. The sulfate ion interacts with Arg-37 which has a cis-peptide conformation, and the magnesium ion interacts with Asp-89, a highly conserved acidic residue in the PRib-PP binding site motif. The XPRT structure also incorporates a feature which has not been observed in other PRTase structures. The C-terminal 12 residues of XPRT adopt an unusual extended conformation and make interactions with a neighboring subunit. The very last residue, Arg-152, could form part of the active site of a symmetry-related subunit in the XPRT tetramer.

Gas-surface interactions in the thermal and sub-thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study the interaction of low-energy Ar atoms with the Ni(001) surface, Angular scattering distributions, in and out of the plane of incidence, are investigated as a function of incident energy, angles of incidence, crystallographic orientation of the incident beam and surface temperature. The results show a clear transition to the structure scattering regime at around 2 eV. However, at lower energies, two sub-regimes are revealed by the simulations, Far energies up to 250 meV, scattering is mainly diffuse, and significant trapping on the surface is observed, At energies above this level, lobular patterns start to form and trapping decreases with the increase in energy, Generally, there is a weak temperature dependence, but variations in the angle of incidence and/or changes in the crystallographic direction, generate significant changes in the scattering patterns.

Solution structure of the sodium channel antagonist conotoxin GS: A new molecular caliper for probing sodium channel geometry

Background: The venoms of Conus snails contain small, disulfide-rich inhibitors of voltage-dependent sodium channels. Conotoxin GS is a 34-residue polypeptide isolated from Conus geographus that interacts with the extracellular entrance of skeletal muscle sodium channels to prevent sodium ion conduction. Although conotoxin GS binds competitively with mu conotoxin GIIIA to the sodium channel surface, the two toxin types have little sequence identity with one another, and conotoxin GS has a four-loop structural framework rather than the characteristic three-loop mu-conotoxin framework. The structural study of conotoxin GS will form the basis for establishing a structure-activity relationship and understanding its interaction with the pore region of sodium channels. Results: The three-dimensional structure of conotoxin GS was determined using two-dimensional NMR spectroscopy. The protein exhibits a compact fold incorporating a beta hairpin and several turns. An unusual feature of conotoxin GS is the exceptionally high proportion (100%) of cis-imide bond geometry for the three proline or hydroxyproline residues. The structure of conotoxin GS bears little resemblance to the three-loop mu conotoxins, consistent with the low sequence identity between the two toxin types and their different structural framework. However, the tertiary structure and cystine-knot motif formed by the three disulfide bonds is similar to that present in several other polypeptide ion channel inhibitors. Conclusions: This is the first three-dimensional structure of a 'four-loop' sodium channel inhibitor, and it represents a valuable new structural probe for the pore region of voltage-dependent sodium channels. The distribution of amino acid sidechains in the structure creates several polar and charged patches, and comparison with the mu conotoxins provides a basis for determining the binding surface of the conotoxin GS polypeptide.

Applying linear time-varying constraints to econometric models: With an application to demand systems

When linear equality constraints are invariant through time they can be incorporated into estimation by restricted least squares. If, however, the constraints are time-varying, this standard methodology cannot be applied. In this paper we show how to incorporate linear time-varying constraints into the estimation of econometric models. The method involves the augmentation of the observation equation of a state-space model prior to estimation by the Kalman filter. Numerical optimisation routines are used for the estimation. A simple example drawn from demand analysis is used to illustrate the method and its application.

Molecular motion in miscible polymer blends .1. Motion in blends of PEO and PVPh studied by solid-state C-13 T-1 rho measurements

Changes in molecular motion in blends of PEO-PVPh have been studied using measurements of C-13 T-1 rho relaxation times. C-13 T-1 rho relaxation has been confirmed as arising from spin-lattice interactions by observation of the variation in T-1 rho with rf field strength and temperature. In the pure homopolymers a minimum in T-1 rho is observed at ca. 50 K above the glass transition temperatures detected by DSC. After blending, the temperature of the minimum in T-1 rho for PEO increased, while that for PVPh decreased, however, the minima, which correspond to the temperatures where the average correlation times for reorientation are close to 3.1 mu s, are separated by 45 K (in a 45% PEO-PVPh blend). These phenomena are explained in terms of the local nature of T-1 rho measurements. The motions of the individual homopolymer chains are only partially coupled in the blend. A short T-1 rho has been observed for protonated aromatic carbons, and assigned to phenyl rings undergoing large-angle oscillatory motion, The effects of blending, and temperature, on the proportion of rings undergoing oscillatory motion are analyzed.

A methodology for current density calculations in high-frequency RF resonators

As nuclear magnetic resonance imaging and spectroscopy move inexorably toward higher field-strength magnets in search of improved signal-to-noise ratio, spectral resolution, and spatial resolution, the way in which radiofrequency (RF) probes are designed changes. At higher frequencies, resonant cavities become the favored RF ''coil'' type and may be built using streamline elements to reduce the inductance of the system. In modeling such systems, the quasi-static approach of assuming that current flows evenly in all conductor cross sections and that adjacent conductors do not affect each other becomes less reasonable. The proximity of RF conductors in resonators typically causes RF eddy currents to flow, whereby the current density in each rung is altered by the RF fields generated by nearby conductors. The proper understanding and prediction of how resonators will perform require a model of the current densities flowing in conducting sections, including all RF eddy current effects. Very few models of this type have been presented in the literature. This article presents an overview of one such model and of how it may be applied to a variety of resonators, both shielded and unshielded, circular, and elliptical, in cross section. Results are presented from a shielded head coil operating at 2 tesla. (C) 1997 John Wiley & Sons, Inc.

Percutaneous absorption of sunscreen agents from liquid paraffin: Self-association of octyl salicylate and effects on skin flux

This study provides an investigation of the availability of octyl salicylate (OS), a common sunscreen agent, from liquid paraffin and the effect of OS on skin permeability. A model membrane system to isolate the vehicle effect from membrane permeability has been developed. Partitioning of OS between liquid paraffin and aqueous receptor phases was conducted. Partition coefficients increased with increase in OS concentration. A range of OS concentrations in liquid paraffin was diffused across human epidermis and synthetic membranes into 4% bovine serum albumin in phosphate-buffered saline and 50% ethanol. Absorption profiles of OS obtained from silicone and low-density polyethylene (LDPE) membranes were similar to each other but higher than for the high-density polyethylene [HDPE (3 times)] membrane and human epidermis (15 times). The steady state fluxes and apparent permeability coefficients (K-p') obtained from the diffusion studies showed the same trends with all membranes, except for the HDPE membrane which showed greater increase in flux and K-p' at concentrations above 30%. IR spectra showed that several bands of OS were shifted with concentrations, and the molecular models further suggested that the main contribution to the self-association is from non-1,4 van der Waals interactions.

Models of alcohol use by young adults: An examination of various attitude-behavior theories

Objective: The aim of this study was to test the effectiveness of various attitude-behavior theories in explaining alcohol use among young adults. The theory of reasoned action (TRA), the theory of planned behavior and an extension of the TRA that incorporates past behavior were compared by the method of maximum-likelihood estimation, as implemented in LISREL for Windows 8.12. Method: Respondents consisted of 122 university students (82 female) who were questioned about their attitudes, subjective norms, perceived behavioral control, past behavior and intentions relating to drinking behavior. Students received course credit for their participation in the research. Results: Overall, the results suggest that the extension of the theory of reasoned action which incorporates past behavior provides the best fit to the data. For these young adults, their intentions to drink alcohol were predicted by their past behavior as well as their perceptions of what important others think they should do (subjective norm). Conclusions: The main conclusions drawn from the research concern the importance of focusing on normative influences and past behavior in explaining young adult alcohol use. Issues regarding the relative merit of various alternative models and the need for greater clarity in the measure of attitudes are also discussed.

Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Virtual plants - integrating architectural and physiological models

Recent advances in computer technology have made it possible to create virtual plants by simulating the details of structural development of individual plants. Software has been developed that processes plant models expressed in a special purpose mini-language based on the Lindenmayer system formalism. These models can be extended from their architectural basis to capture plant physiology by integrating them with crop models, which estimate biomass production as a consequence of environmental inputs. Through this process, virtual plants will gain the ability to react to broad environmental conditions, while crop models will gain a visualisation component. This integration requires the resolution of the fundamentally different time scales underlying the approaches. Architectural models are usually based on physiological time; each time step encompasses the same amount of development in the plant, without regard to the passage of real time. In contrast, physiological models are based in real time; the amount of development in a time step is dependent on environmental conditions during the period. This paper provides a background on the plant modelling language, then describes how widely-used concepts of thermal time can be implemented to resolve these time scale differences. The process is illustrated using a case study. (C) 1997 Elsevier Science Ltd.

Non-equilibrium energy and momentum accommodation coefficients of Ar atoms scattered from Ni(001) in the thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study energy and momentum transfer of low-energy Ar atoms scattered from the Ni(001) surface. The investigation concentrates on the dependence of these processes on incident energy, angles of incidence and surface temperature. Energy transfer exhibits a strong dependence on the surface temperature, at incident energies below 500 meV, and incident angles close to specular incidence. Above 500 meV, the surface temperature dependence vanishes, and a limiting value in the amount of energy transferred to the surface is attained. Momentum exchange is investigated in terms of tangential and normal components. Both components exhibit a weak surface temperature dependence, but they have opposite behaviours at all incidence angles. In each component, momentum can be lost or gained following the interaction with the surface. (C) 1997 Elsevier Science B.V.

In vivo effects of chicken interferon-gamma during infection with Eimeria

Newly hatched chickens are highly susceptible to infection by opportunistic pathogens during the first 1 or 2 weeks of life, The use of cytokines as therapeutic agents has been studied in animal models as well as in immunosuppressed patients, This approach has become more feasible in livestock animals, in particular poultry, with the recent cloning of cytokine genes and the development of new technologies, such as live delivery vectors, We have recently cloned the gene for chicken interferon-gamma (Ch-IFN-gamma), Poly-HIS-tagged recombinant Ch-IFN-gamma was expressed in Escherichia coil, was purified by Ni chromatography, and was found to be stable at 4 degrees C and an ambient temperature for at least several months and Several weeks, respectively, Ch-IFN-gamma was capable of protecting chick fibroblasts from undergoing virus-mediated lysis, induced nitrite secretion from chicken macrophages in vitro, and enhanced MHC class II expression on macrophages, Administration of recombinant Ch-IFN-gamma to chickens resulted in enhanced weight gain over a 12-day period, Furthermore, the therapeutic potential of Ch-IFN-gamma was assessed using a coccidial challenge model, Birds were treated with Ch-IFN-gamma or a diluent control and then infected with Eimeria acervulina. Infected birds treated with Ch-IFN-gamma showed improved weight gain relative to noninfected birds, The ability of Ch-IFN-gamma to enhance weight gain in the face of coccidial infection makes it an excellent candidate as a therapeutic agent.

A defense of backwards in time causation models in quantum mechanics

This paper offers a defense of backwards in time causation models in quantum mechanics. Particular attention is given to Cramer's transactional account, which is shown to have the threefold virtue of solving the Bell problem, explaining the complex conjugate aspect of the quantum mechanical formalism, and explaining various quantum mysteries such as Schrodinger's cat. The question is therefore asked, why has this model not received more attention from physicists and philosophers? One objection given by physicists in assessing Cramer's theory was that it is not testable. This paper seeks to answer this concern by utilizing an argument that backwards causation models entail a fork theory of causal direction. From the backwards causation model together with the fork theory one can deduce empirical predictions. Finally, the objection that this strategy is questionable because of its appeal to philosophy is deflected.