Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Frequency-Dependent Streaming Potentials

An experimental apparatus and data acquisition system was constructed to measure the streaming potential coupling coefficients as a function of frequency. The purpose of the experiments was to measure, for the first time, the real and imaginary portion of streaming potentials. In addition, the measured frequency range was extended beyond any previous measurements. Frequency-dependent streaming potential experiments were conducted on one glass capillary and two porous glass filters. The sample pore diameters ranged from 1 mm to 34 μm. Two frequency-dependent models (Packard and Pride) were compared to the data. Both Pride's and Packard's models have a good fit to the experimental data in the low- and intermediate-frequency regime. In the high-frequency regime, the data fit the theory after being corrected for capacitance effects of the experimental setup. Pride's generalized model appears to have the ability to more accurately estimate pore sizes in the porous medium samples. Packard's model has one unknown model parameter while Pride's model has four unknown model parameters, two of which can be independently determined experimentally. Pride's additional parameters may allow for a determination of permeability. Copyright 2001 Academic Press.     

Modeling study of non-line-narrowed hole-burned spectra in weakly coupled dimers and multi-chromophoric molecular assemblies

Several different models have been proposed to explain the origin of the complex anti-hole features observed in hole-burned (HB) spectra of excitonically coupled systems such as photosynthetic complexes. This lack of consensus presents a serious constraint on the interpretation of HB spectra and the underlying electronic structures of these systems. To resolve this problem we present results of modeling studies of non-resonant HB spectra taking uncorrelated excitation energy transfer and excitonic interactions into account. Simplified analytical results are compared with Monte Carlo simulations in which excitonic interactions are explicitly taken into account in order to disentangle a number of distinct effects. It is shown that these effects can accurately account for both hole shapes and the broad anti-hole structure observed in excitonically coupled systems. We argue that these models will provide a necessary framework for probing the electronic structure of these systems via HB spectroscopy.     

Studies on photoinduced effects in pulse-electrodeposited Ag/Hg-1212/CdSe hetero-nanostructures

Metal/superconductor/semiconductor (Ag/Hg-1212/CdSe) hetero-nanostructures have been fabricated using pulse-electrodeposition technique and are characterized by X-ray diffraction (XRD), full-width at half-maximum (FWHM) and scanning electron microscopy (SEM) studies. The junction capacitance of Ag/Hg-1212, Hg-1212/CdSe and Ag/Hg-1212/CdSe heterojunctions is measured in dark and under laser irradiation at room temperature. The nature of the junction formed and built-in-junction potentials were determined. The increase in carrier concentration across the junction due to photo-irradiation has been observed.     

Effect of laser irradiation of C-V characteristics of electrodeposited Ag/Tl-2223/CdSe hetero-nanostructures

One of the innovative technological directions for the high-temperature superconductors has been persued by fabricating the heteroepitaxial multilayer structures such as superconductor-semiconductor heterostructures. In the present investigation, metal/superconductor/semiconductor (Ag/Tl-2223/CdSe) hetero-nanostructures have successfully been fabricated using dc electrodeposition technique and were characterized by X-ray diffraction (XRD), full-width at half-maximum (FWHM) and scanning electron microscopy (SEM) studies. The measurement of junction capacitance as a function of biasing voltage was used for the estimation of junction built-in-potential (V _D) and to study the charge distribution in a heterojunction. The Mott-Schottky plots were measured for each junction in dark and under the photo-irradiation. The effect of laser irradiation on C-V characteristics of hetero-nanostructure has been studied.     

Glycopeptide and Oligosaccharide Libraries

Despite the burgeoning interest in the various biological functions and consequent therapeutic potential of the vast number of oligosaccharides found in nature on glycoproteins and cell surfaces, the development of combinatorial carbohydrate chemistry has not progressed as rapidly as expected. The reason for this imbalance is rooted in the difficulty of oligosaccharide assembly and analysis that renders synthesis a rather cumbersome endeavor. Parallel approaches that generate series of analogous compounds rather than real libraries have therefore typically been used. Since generally low affinity is obtained for interactions between carbohydrate receptors and modified oligosaccharides designed as mimetics of natural carbohydrate ligands, glycopeptides have been explored as alternative mimics. Glycopeptides have been proven in many cases to be superior ligands with higher affinity for a receptor than the natural carbohydrate ligand. High-affinity glycopeptide ligands have been found for several types of receptors including the E-, P-, and L-selectins, toxins, glycohydrolases, bacterial adhesins, and the mannose-6-phosphate receptor. Furthermore, the assembly of glycopeptides is considerably more facile than that of oligosaccharides and the process can be adapted to combinatorial synthesis with either glycosylated amino acid building blocks or by direct glycosylation of peptide templates. The application of the split and combine approach using ladder synthesis has allowed the generation of very large numbers of compounds which could be analyzed and screened for binding of receptors on solid phase. This powerful technique can be used generally for the identification and analysis of the complex interaction between the carbohydrates and their receptors.     

Frequency-dependent electroosmosis

This paper presents a theory for frequency-dependent electroosmosis. It is shown that for a closed capillary the electroosmosis frequency-dependent ratio of DeltaV/DeltaP is constant with increasing frequency until inertial effects become prevalent, at which time DeltaV/DeltaP starts to decrease with increasing frequency. The frequency response of the electroosmosis coupling coefficient is shown to be dependent on the capillary radius. As the capillary radius is made smaller, inertial effects start to occur at higher frequencies. As part of this paper, frequency-dependent electroosmosis is compared to frequency-dependent streaming potentials. In this comparison it is shown that inertial effects start to become more prevalent at higher frequencies for the closed capillary frequency-dependent electroosmosis case than for the frequency-dependent streaming potential case in the same capillary. It is also shown that this difference is due to a second viscosity (transverse) wave that emanates from the velocity zero within the capillary for the electroosmosis case. The second viscosity wave superposes with the viscosity wave that emanates from wall of the capillary to effectively reduce the hydraulic radius of the capillary. Data are presented for a 0.127-mm capillary to support the findings in this paper.     

Temperature dependence of hole growth kinetics in aluminum-phthalocyanine-tetrasulfonate in hyperquenched glassy water

The temperature (T) dependence of hole growth kinetics (HGK) data that span more than four decades of burn fluence are reported for aluminum-phthalocyanine tetrasulfonate (APT) in fresh and annealed hyperquenched glassy water (HGW) for temperatures between 5 and 20 K. The highly dispersive HGK data are modeled by using the "master" equation based on the two level system (TLS) model described in 2000 by Reinot and Small [J. Chem. Phys. 2000, 113, 10207]. We have demonstrated that thermal line broadening is not enough to account for temperature-dependent HGK for temperatures greater than 10 K. To overcome the discrepancy, the hole growth model must account for thermal hole filling (THF) processes. For the first time, the "master" equation used for HGK simulations is modified to take into account both the temperature dependence of the (single site) absorption spectrum and THF processes, effectively turning off those TLS which do not participate in the hole burning process at higher temperatures. A single set of parameters, some of which were determined directly from the hole spectra, was found to provide satisfactory fits to the HGK data for APT in fresh and annealed HGW for holes burned in the 679.7-676.9 nm range from the high to low energy sides of the Qx absorption band. Furthermore, we propose that HGK modeling at high burn fluences requires that the TLS model be further modified to take into account the existence of extrinsic multiple level systems.