Dynamic simulations of the molecular conformations of wild type and mutant xanthan polymers suggest that conformational differences may contribute to observed differences in viscosity

Xanthan gum is an exopolysaccharide secreted by the bacterium Xanthamonas campestris whose ability to make solutions viscous at low concentrations and over a pH and temperature range have generated much interest in both academic and industrial environments. Mutant Xanthamonas strains have been derived that produce xanthan gums with an altered or variant subunit chemical structure and different measured viscosities when compared with the wild type (wt) form of the polymer. Two variant gums were targeted as potentially interesting in this study, these being the nonacetylated tetramer (natet) and the acetylated tetramer (atet), which both lack a side-chain terminal mannose residue and in one case (natet) lacks an acetate group on an internal mannose residue. Solutions of these tetrameric gums possess viscosities higher (natet) and lower (atet) than the wt gum, and therefore we have attempted to determine whether these molecules possess unique conformational preferences when compared with the wt and with each other. In this manner we can initiate an understanding of how a polysaccharide's conformation contributes to its solution properties. The GEGOP software permits a sampling of the static and dynamic equilibrium states of carbohydrate molecules, and this software was employed to calculate equilibrium states of representative oligosaccharides with chemical structures representative of xanthan-like molecules. Energy minimization techniques revealed similar local minima for all three molecules. Some of these minima are comprised of elongate backbone conformations (A type) in which side chains fold onto backbone surfaces. Other minima with A backbones possessed side chains in less intimate backbone contact especially when calculations were performed with a low dielectric constant. This phenomenon was particularly pronounced in the wt molecule where an increased number of negatively charged side-chain residues experience charge repulsion resulting in reduced side-chain-backbone contact. Metropolis Monte Carlo (MMC) dynamic simulations performed with an elevated temperature factor (1000 K) allowed a better qualitative representation of conformational space than 300 K simulations. Employing a nonhierarchical cluster analysis method (population density profile: PDP) coupled with a classification scheme, it was possible to partition resulting MMC data sets into conformational families. This analysis revealed that in simulations performed with different dielectric constant values (10, 25, and infinity) all molecules possessed primarily A-type backbones. Less elongate, more open helical backbone forms (B, C, D, J, and Flat-a) did occur during the simulations but were populated to a lesser extent. In the natet molecule significantly open helical backbones existed (E, F, G, H, and I) that did not occur in the lower viscosity wt and atet molecules. PDP clustering methods and subsequent conformational classification applied to the first residue (mannose) of the side chain permitted a determination of side-chain orientation. Comparison of all three molecules indicated a larger population of side-chain conformational families in less direct backbone contact for the wt molecule than either of the variant molecules (natet/atet) suggesting that the side chains in the wt are more flexible. Thus, a major conformational difference between the high viscosity natet and the lower viscosities of the wt/atet is the increased amount of open helical backbone in the natet. In addition, the significant difference between the higher viscosity wt and the lower viscosity atet is the increase side-chain flexibility in the wt. We hypothesize that conformational differences of this kind could form a partial explanation of the observed differences in viscosity between these xanthan-like polymers.     

Identification of glycoprotein 330 as an endocytic receptor for apolipoprotein J/clusterin

Glycoprotein 330 (gp330) is a member of a family of endocytic receptors related to the low density lipoprotein receptor. gp330 has previously been shown to bind a number of ligands in common with its family member, the low density lipoprotein receptor-related protein (LRP). To identify ligands specific for gp330 and relevant to its localization on epithelia such as in the mammary gland, gp330-Sepharose affinity chromatography was performed. As a result, a 70-kDa protein was selected from human milk and identified by protein sequencing to be apolipoprotein J/clusterin (apoJ). Solid-phase binding assays confirmed that gp330 bound to apoJ with high affinity (Kd = 14.2 nM). Similarly, gp330 bound to apoJ transferred to nitrocellulose after SDS-polyacrylamide gel electrophoresis. LRP, however, showed no binding to apoJ in either type of assay. The binding of gp330 to apoJ could be competitively inhibited with excess apoJ as well as with the gp330 ligands apolipoprotein E, lipoprotein lipase, and the receptor-associated protein, a 39-kDa protein that acts to antagonize binding of all known ligands for gp330 and LRP. Several cultured cell lines that express gp330 and ones that do not express the receptor were examined for their ability to bind and internalize 125I-apoJ. Only cells that expressed gp330 endocytosed and degraded radiolabeled apoJ. Furthermore, F9 cells treated with retinoic acid and dibutyryl cyclic AMP to increase expression levels of gp330 displayed an increased capacity to internalize and degrade apoJ. Cellular internalization and degradation of radiolabeled apoJ could be inhibited with unlabeled apoJ, receptor-associated protein, and gp330 antibodies. The results indicate that gp330 but not LRP can bind to apoJ in vitro and that gp330 expressed by cells can mediate apoJ endocytosis leading to lysosomal degradation.     

Closed-loop expressions of minimum energy control for single-inputlinear digital systems

Closed-loop expressions for the minimum energy control of a single-input linear digital system are described. They are obtained by two different methods. The optimal inputs are given by state feedback with the bounded variable gains. The gains are independent of the initial state of the system     

Correlation of the leakage current and charge pumping in silicon oninsulator gate-controlled diodes

The leakage and charge pumping currents were measured in gate-controlled MOS p-i-n diodes fabricated on thin SIMOX substrates. The efficiencies of the techniques as well as their complementary features are analyzed for various experimental conditions. The interface properties of device-grade SIMOX wafers are characterized and shown to be compatible with VLSI requirements. Special interface coupling effects, which occur only in fully depleted SOI devices and modify the conventional signature of charge pumping and leakage current, are thoroughly investigated     

An efficient technique for detecting catastrophic convolutional codes

Catastrophic convolutional codes (CC) cause an infinite number of decoded data bit errors when decoding a finite number of code symbols. A CC displays a catastrophic error propagation if the generating polynomials have a common factor. An efficient algorithm for polynomial factorization in GF(2^m) is used for detecting catastrophic CC for any rate n/m and constraint length k. A general formula is derived to calculate the number of catastrophic codes in any (m, n, k) CC.     

Modeling and analysis of vias in multilayered integrated circuits

A method for modeling and analyzing vias the multilayered integrated circuits is presented. The model is based on microwave network theory. The whole via structure is divided into cascaded subnetworks, including a vertical via passing through different layers and transitions from the microstrip line and/or striplines to the vertical via. The parameters of each subnetwork are obtained from electromagnetic field analysis. Numerical results in the frequency domain and the time domain are presented. Validation of the model has been carried out by both measurements and finite-difference-time-domain (FDTD) modeling. The results show good agreement with the measurements in the frequency range for which the components of the experimental model are within specification. The time domain simulation results also agree well with the FDTD results     

Comment and discussion on digital processing of PD pulses

Some of the more salient aspects of the digital processing technology of PD signals are examined. Most of the efforts in this field are concentrated on the application of digital analyzers for pulse height analysis, pattern recognition and identification of the physical phenomena. It is demonstrated that errors in the signal processing unit can lead to dominant mistakes in the interpretation of the test results     

An engineering equation for corona devices

Engineers who either design or apply any charge-generating device are faced with characterizing the charge output of their device. This charge output per unit time is the net current output of the device. Such devices are referred to as corona-generating devices, corona chargers, or simply corona devices, and unfortunately they do not follow Ohm's Law; instead these devices display a nonlinear IV or current-voltage curve. This article deals with the development of a nonlinear IV equation that allows the characterization of the device over a large voltage range. To obtain the equation the unipolar charge injection equation is modified to account for the potential necessary to create charge injection. For a gas this potential is shown to be equal to the corona onset potential. The resulting equation is applied to some data discussed by Schaffert in his book on electrophotography and to new data from corona wires at high positive potential. Good agreement is obtained both near and away from the onset potential. The equation suggests that in the charge injection region the resistance is linearly related to the length of the injection region. The new corona data supports this hypothesis. The data also indicates the charge development region is fixed for a given geometry     

A comparison of two conformal methods for FDTD modeling

Two conformal finite-difference time-domain (FDTD) methods are considered, the contour path (CPFDTD) method of Jurgens et al. (see IEEE Trans. Antennas Propagat., vol.40, p.357, 1992) and the overlapping grid (OGFDTD) method of Yee et al. (see IEEE Trans. Antennas Propagat., vol.40, p.1068, 1992). Both TE and TM scattering from a two-dimensional (2-D), perfectly conducting circular cylinder are used to test the accuracy of the methods for curved surfaces. Also, TE and TM scattering from a 2-D, perfectly-conducting rotated square cylinder are used to test the accuracy for corners and edges. It is shown that the conformal method proposed by Yee et al. provide significant improvement in accuracy over the original FDTD algorithm for most of the geometries studied. However, implementation becomes more difficult as the geometries become more complex. The conformal method proposed by Jurgens et al. provide significant improvement in accuracy as well for most of the geometries studied. However, improvement does not occur for the TM case when the square cylinder is not aligned properly with the grid. Implementation of the CPFDTD method is relatively straightforward. For the majority of the cases studied, the OGFDTD method is more accurate than the CPFDTD method     

Opsin/all-trans-retinal complex activates transducin by different mechanisms than photolyzed rhodopsin

In rhodopsin, the 11-cis-retinal chromophore forms a complex with Lys296 of opsin via a protonated Schiff base. Absorption of light initiates the activation of rhodopsin by cis/trans photoisomerization of retinal. Thermal relaxation through different intermediates leads into the metarhodopsin states which bind and activate transducin (Gt) and rhodopsin kinase (RK). all-trans-Retinal also recombines with opsin independent of light, forming activating species of the receptor. In this study, we examined the mechanism by which all-trans-retinal activates opsin. To exclude other amines except active site Lys296 from formation of Schiff bases, we reductively methylated rhodopsin (PM-rhodopsin), which we then bleached to generate PM-opsin. Using spectroscopic methods and a Gt activation assay, we found that all-trans-retinal interacted with PM-opsin, producing a noncovalent complex that activated Gt. The residual nucleotide exchange in Gt catalyzed by opsin was approximately 1/250 lower relative to that of photoactivated rhodopsin (pH 8.0, 23 degrees C). Addition of equimolar all-trans-retinal led to an occupancy of one-tenth of the putative retinal binding site(s) of opsin and enhanced the Gt activation rate 2-fold. When the concentration of all-trans-retinal was increased to saturation, the Gt activation rate of the opsin/all-trans-retinal complex was approximately 1/33 lower compared to that of photoactivated rhodopsin. We conclude that all-trans-retinal can form a noncovalent complex with opsin that activates Gt by different mechanisms than photolyzed rhodopsin.