Mechanisms of virus assembly probed by Raman spectroscopy: the icosahedral bacteriophage P22

A microdialysis flow cell has been developed for time-resolved Raman spectroscopy of biological macromolecules and their assemblies. The flow cell permits collection of Raman spectra concurrent with the efflux of small solute molecules into a solution of macromolecules and facilitates real-time spectroscopic detection of structural transitions induced by the effluent. Additionally, the flow cell is well suited to the investigation of hydrogen-isotope exchange phenomena that can be exploited as dynamic probes of viral protein folding and solvent accessibility along the assembly pathway. Here, we describe the application of the Raman dynamic probe to the maturation of the icosahedral capsid of bacteriophage P22, a double-stranded DNA virus. The P22 virion is constructed from a capsid precursor (procapsid) consisting of 420 coat subunits (gp5) in an outer shell and a few hundred scaffolding subunits (gp8) within. Capsid maturation involves expulsion of scaffolding subunits coupled with shell expansion at the time of DNA packaging. Raman static and dynamic probes reveal that the scaffolding subunit is highly alpha-helical and highly thermolabile, and lacks a typical hydrophobic core. When bound within the procapsid, the alpha-helical fold of gp8 is thermostabilized; however, this stabilization confers no apparent protection against peptide NH-->ND exchange. A molten globule model is proposed for the native scaffolding subunit that functions in procapsid assembly. Accompanying capsid expansion, a small conformational change (alpha-helix-->beta-strand) is also observed in the coat subunit. Domain movement mediated by hinge bending is proposed as the mechanism of capsid expansion. On the basis of these results, a molecular model is proposed for assembly of the P22 procapsid.     

Semi-Markov models with an application to power-plant reliabilityanalysis

Systems with, (1) a finite number of states, and (2) random holding times in each state, are often modeled using semi-Markov processes. For general holding-time distributions, closed formulas for transition probabilities and average availability are usually not available. Recursion procedures are derived to approximate these quantities for arbitrarily distributed holding-times; these recursion procedures are then used to fit the semi-Markov model with Weibull distributed holding-times to actual power-plant operating data. The results are compared to the more familiar Markov models; the semi-Markov model using Weibull holding-times fits the data remarkably well. In particular comparing the transition probabilities shows that the probability of the system being in the state of refitting converges more quickly to its limiting value as compared to convergence in the Markov model. This could be because the distribution of the holding-times in this state is rather unlike the exponential distribution. The more flexible semi-Markov model with Weibull holding-times describes more accurately the operating characteristics of power-plants, and produces a better fit to the actual operating data     

The effect of alumina particulate morphology on the properties of reinforced poly(propylene) and poly(ethylene-co-vinyl acetate) composites

The effect of alumina particulates on a thermoplastic matrix is investigated, in particular the effect altering the alumina particle size and morphology has on the mechanical properties. Different grades of alumina are used and two thermoplastic matrices; namely poly(propylene) and poly(ethylene-co-vinyl acetate). Investigations showed that optimum properties were achieved with the alumina of smallest particle size and lowest aspect ratio. Preliminary work has also been performed on the use of silane coupling agents and they have proved effective in increasing the tensile properties of the composites.     

Effect of Microstructure on the Accelerated Creep of 20CrMoV12‐1 and P 91 Steels

In the initial part the change of microstructure for steel X20 CrMoV 121 is discussed in terms of the distribution of carbide precipitates and its effects on accelerated creep resistance and hardness are presented. In the following, experimental results of microstructure and accelerated creep resistance are presented for the steels X20CrMoV 121 and P91 annealed for up to 8760 hours at 650°C and 750°C before the testing. A similar evolution of the distribution of carbide particles of a size above 102 nm is found for both steels, while the accelerated creep resistance is diminished much stronger for the steel X20CrMoV 121. This difference is due to a greater stability of NbC than that of VC precipitates, both related to the evolution of the chemical composition of complex chromium, molybdenum and iron carbide particles.     

Electrochemical studies of octadecanethiol and octanethiol films on variable surface area mercury sessile drops

Octadecanethiol (ODT) and octanethiol (OT) films at the mercury-electrolyte interface are examined using cyclic voltammetry and differential capacitance measurements at a single frequency. A mercury flow-system is used to alter the volume, and therefore, the surface area and surface pressure of the mercury electrode. Manipulation of the mercury electrode's volume enables the introduction and removal of defects in the insulating thiol films. OT and ODT film behavior are contrasted under conditions of expansion and contraction. ODT forms extremely impermeable layers that allow 1000 time less redox probe current than seen on uncoated drops. Expansion of the mercury electrode to increase the electrode surface area produces defects and pinholes in the thiol film. These defects are almost completely removed when the drop is compressed back to its initial surface area. OT also forms insulating films on mercury sessile drops, however these films contain more defects than ODT films. While expansion of an OT-coated mercury drop increases redox probe current, recompression of the drop does not return the film to its initial condition. Pinholes and defects in the OT and ODT films can also be produced by cycling to negative potentials, which produce abrupt stripping peaks.     

Online segmentation of time series based on polynomial least-squares approximations

The paper presents SwiftSeg, a novel technique for online time series segmentation and piecewise polynomial representation. The segmentation approach is based on a least-squares approximation of time series in sliding and/or growing time windows utilizing a basis of orthogonal polynomials. This allows the definition of fast update steps for the approximating polynomial, where the computational effort depends only on the degree of the approximating polynomial and not on the length of the time window. The coefficients of the orthogonal expansion of the approximating polynomial-obtained by means of the update steps-can be interpreted as optimal (in the least-squares sense) estimators for average, slope, curvature, change of curvature, etc., of the signal in the time window considered. These coefficients, as well as the approximation error, may be used in a very intuitive way to define segmentation criteria. The properties of SwiftSeg are evaluated by means of some artificial and real benchmark time series. It is compared to three different offline and online techniques to assess its accuracy and runtime. It is shown that SwiftSeg-which is suitable for many data streaming applications-offers high accuracy at very low computational costs.     

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.