Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.     

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.     

Ultra-low-loss inverted taper coupler for silicon-on-insulator ridge waveguide

An ultra-low-loss coupler for interfacing a silicon-on-insulator ridge waveguide and a single-mode fiber in both polarizations is presented. The inverted taper coupler, embedded in a polymer waveguide, is optimized for both the transverse-magnetic and transverse-electric modes through tapering the width of the silicon-on-insulator waveguide from 450 nm down to less than 15 nm applying a thermal oxidation process. Two inverted taper couplers are integrated with a 3-mm long silicon-on-insulator ridge waveguide in the fabricated sample. The measured coupling losses of the inverted taper coupler for transverse-magnetic and transverse-electric modes are ∼ 0.36 dB and ∼ 0.66 dB per connection, respectively.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

Heuristics for container loading of furniture

We consider a container loading problem that occurs at a typical furniture manufacturer. Each furniture item has an associated profit. Given container dimensions and a set of furniture items, the problem is to determine a subset of items with maximal profit sum that is loadable in the container. In the studied company, the problem arises hundreds of times daily during transport planning. Instances may contain more than one hundred different items with irregular shapes. To solve this complex problem we apply a set of heuristics successively that each solve one part of the problem. Large items are combined in specific structures to ensure proper protection of the items during transportation and to simplify the problem. The solutions generated by the heuristic has an average loading utilization of 91.3% for the most general instances with average running times around 100 seconds.     

The radiation degradation of a nanotube-polyimide nanocomposite

The radiation degradation of a nanotube-polyimide nanocomposite was studied. Radiation chemistry was observed that was not present in the unmodified polymer or in the imbedded single-walled carbon nanotubes (SWNTs) themselves. The tensile properties were found to be improved by the addition of SWNTs in the unirradiated materials, and no deterioration in these properties with irradiation was observed. The SWNTs were found to have a detrimental effect on the optical properties however. The transparency of the composite was degraded significantly faster by electron-beam radiation than the neat polymer was. This may make the SWNT/polyimide composites unsuitable for some space applications. Electron Spin Resonance (ESR) measurements determined that the SWNTs interfere with the radical chemistry in the irradiated materials. This could be due to energy dissipation by the SWNT network, preventing the formation of radical species, or alternatively, preferential reaction or termination of radicals by the nanotubes. FT-Raman spectroscopy was found to be a very useful tool for examining SWNTs embedded at low concentrations. It revealed no signs of SWNT degradation up to 10 MGy.     

Hierarchical zeolites: enhanced utilisation of microporous crystals in catalysis by advances in materials design

The introduction of synthetic zeolites has led to a paradigm shift in catalysis, separations, and adsorption processes, due to their unique properties such as crystallinity, high-surface area, acidity, ion-exchange capacity, and shape-selective character. However, the sole presence of micropores in these materials often imposes intracrystalline diffusion limitations, rendering low utilisation of the zeolite active volume in catalysed reactions. This critical review examines recent advances in the rapidly evolving area of zeolites with improved accessibility and molecular transport. Strategies to enhance catalyst effectiveness essentially comprise the synthesis of zeolites with wide pores and/or with short diffusion length. Available approaches are reviewed according to the principle, versatility, effectiveness, and degree of reality for practical implementation, establishing a firm link between the properties of the resulting materials and the catalytic function. We particularly dwell on the exciting field of hierarchical zeolites, which couple in a single material the catalytic power of micropores and the facilitated access and improved transport consequence of a complementary mesopore network. The carbon templating and desilication routes as examples of bottom-up and top-down methods, respectively, are reviewed in more detail to illustrate the benefits of hierarchical zeolites. Despite encircling the zeolite field, this review stimulates intuition into the design of related porous solids (116 references).     

Coupling Microplate-Based Antibacterial Assay with Liquid Chromatography for High-Resolution Growth Inhibition Profiling of Crude Extracts: Validation and Proof-of-Concept Study with Staphylococcus aureus

With the identification of novel antibiotics from nature being pivotal in the fight against human pathogenic bacteria, there is an urgent need for effective methodologies for expedited screening of crude extracts. Here we report the development and validation of a simple and dye-free antimicrobial assay in 96-well microplate format, for both determination of IC₅₀ values and high-resolution inhibition profiling to allow pin-pointing of bioactive constituents directly from crude extracts. While commonly used antimicrobial assays visualize cell viability using dyes, the developed and validated assay conveniently uses OD₆₀₀ measurements directly on the fermentation broth. The assay was validated with an investigation of the inhibitory activity of DMSO against Staphylococcus aureus, temperature robustness, interference by coloured crude extracts as well as inter-day reproducibility. The potential for high-resolution S. aureus growth inhibition profiling was evaluated on a crude extract of an inactive Alternaria sp., spiked with ciprofloxacin.     

Intraventricular dispersion and temporal delay of early left ventricular filling after acute myocardial infarction. Assessment by magnetic resonance velocity mapping

This article aims to describe early left ventricular diastolic inflow using magnetic resonance velocity mapping in patients with recent acute myocardial infarction and in normal volunteers. Magnetic resonance velocity mapping was performed in a long axis plane through the hearts of 46 patients with recent, first time acute myocardial infarction and 43 age-matched normal volunteers. The peak velocities at six levels of the early diastolic inflow stream were recorded. A velocity index was calculated as the peak velocity in each position relative to the peak velocity at the mitral leaflet tips. Also, the temporal delay of velocity propagation was computed. Velocity index 4 cm downstream of mitral leaflet tips was lower in the acute myocardial infarction group (0.42 (0.17)) (mean (SD)) compared to controls (0.59 (0.25)) (p < 0.001). Temporal delay in the same position was longer in the acute myocardial infarction group (62 (67) ms) than in controls (32 (39) ms) (p < 0.02). Blood flow patterns in patients after acute myocardial infarction were characterized by increased dispersion of velocities and increased temporal delay of velocity propagation, probably reflecting impaired active left ventricular relaxation. Intraventricular flow measurements constitute a promising new technique for non-invasive assessment of left ventricular diastolic function.