Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics

Determining the structure of the (oligomeric) intermediates that form during the self-assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo-induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid-forming peptide, Aβ_16-22. A PIC amino acid containing a trifluormethyldiazirine (TFMD) group—Fmoc(TFMD)Phe—was incorporated into the sequence (Aβ*_16–22). Electrospray ionization ion-mobility spectrometry mass-spectrometry (ESI-IMS-MS) analysis of the PIC products confirmed that Aβ*_16–22 forms assemblies with the monomers arranged as anti-parallel, in-register β-strands at all time points during the aggregation assay. The assembly process was also monitored separately using fluorescence quenching to profile the fibril assembly reaction. The molecular picture resulting from discontinuous molecule dynamics simulations showed that Aβ_16-22 assembles through a single-step nucleation into a β-sheet fibril in agreement with these experimental observations. This study provides detailed structural insights into the Aβ_16-22 self-assembly processes, paving the way to explore the self-assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease.     

Extrusion of highly filled flexible polymer sheet

Highly-filled polymer systems include color masterbatches, feedstocks for powder injection molding, and rigid sheets with high levels of flame retardants, but they have not been explored for flexible sheet. This work investigated the (a) selecting a polymer matrix with enough melt strength and flexibility to form a stable sheet with high filler loading, (b) the maximum achievable filler loading for the sheet, and (c) optimizing the process of extruding a highly-filled flexible polymer system. Extrusion grade low-density polyethylene (LDPE) provided sufficient flexibility and permitted a maximum filler loading of 36 vol% (~78 wt%). Good dispersion of the nanoparticle filler, however, required two passes through multiple screw extruders and a small reduction in the viscosity of the LDPE. Sheet with thickness of 415 μm, surface roughness of <1 μm, and sufficient flexibility was extruded continuously at a rate of 10 m/min., but it required a more traditional coat hanger manifold to prevent filler hang up in the sheet die. The filler particles were distributed uniformly through the core and skin of the sheet, giving the sheet good mechanical properties.     

Study of the catalytic combustion of lean hydrogen-air mixtures in a monolith reactor

This paper presents an experimental study of catalytic hydrogen combustion that used commercial catalysts containing Pt in a honeycomb monolith reactor in a plug flow configuration. The emphasis is on determining global kinetics in the case of low hydrogen content. Measurements of the temperature and composition of the reaction product at the outlet in the steady state condition at the different initial compositions of hydrogen and total volumetric feed rates were performed. The conversion of hydrogen was determined in parallel to the composition of the reaction product at the outlet using GC as well as by means of the thermodynamic approach using material and energy balances. The influence of the flow rate and initial molar fraction of hydrogen on hydrogen conversion is shown. A kinetic expression of the Arrhenius type is proposed with the reaction first order in hydrogen and zero order in oxygen for the overall process of the oxidation of hydrogen in lean hydrogen-air mixtures. The determined activation energy was in good agreement with the desorption activation energy for O₂ from graphene-covered Pt(111) surfaces using temperature-programmed desorption. This result shows transport-limitations for heterogeneous hydrogen conversion in catalytic hydrogen combustion.     

Ubiquitin C-Terminal Hydrolase L1: Biochemical and Cellular Characterization of a Covalent Cyanopyrrolidine-Based Inhibitor

The deubiquitinase (DUB) ubiquitin C-terminal hydrolase L1 (UCHL1) is expressed primarily in the central nervous system under normal physiological conditions. However, UCHL1 is overexpressed in various aggressive forms of cancer with strong evidence supporting UCHL1 as an oncogene in lung, glioma, and blood cancers. In particular, the level of UCHL1 expression in these cancers correlates with increased invasiveness and metastatic behavior, as well as poor patient prognosis. Although UCHL1 is considered an oncogene with potential as a therapeutic target, there remains a significant lack of useful small-molecule probes to pharmacologically validate in vivo targeting of the enzyme. Herein, we describe the characterization of a new covalent cyanopyrrolidine-based UCHL1 inhibitory scaffold in biochemical and cellular studies to better understand the utility of this inhibitor in elucidating the role of UCHL1 in cancer biology.     

Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors

Bile acids have been reported as important cofactors promoting human and murine norovirus (NoV) infections in cell culture. The underlying mechanisms are not resolved. Through the use of chemical shift perturbation (CSP) NMR experiments, we identified a low-affinity bile acid binding site of a human GII.4 NoV strain. Long-timescale MD simulations reveal the formation of a ligand-accessible binding pocket of flexible shape, allowing the formation of stable viral coat protein–bile acid complexes in agreement with experimental CSP data. CSP NMR experiments also show that this mode of bile acid binding has a minor influence on the binding of histo-blood group antigens and vice versa. STD NMR experiments probing the binding of bile acids to virus-like particles of seven different strains suggest that low-affinity bile acid binding is a common feature of human NoV and should therefore be important for understanding the role of bile acids as cofactors in NoV infection.     

Challenges in forming inferences from limited data: a case study of malaria parasite maturation

Inferring biological processes from population dynamics is a common challenge in ecology, particularly when faced with incomplete data. This challenge extends to inferring parasite traits from within-host infection dynamics. We focus on rodent malaria infections (Plasmodium berghei), a system for which previous work inferred an immune-mediated extension in the length of the parasite development cycle within red blood cells. By developing a system of delay-differential equations to describe within-host infection dynamics and simulating data, we demonstrate the potential to obtain biased estimates of parasite (and host) traits when key biological processes are not considered. Despite generating infection dynamics using a fixed parasite developmental cycle length, we find that known sources of measurement bias in parasite stage and abundance data can affect estimates of parasite developmental duration, with stage misclassification driving inferences about extended cycle length. We discuss alternative protocols and statistical methods that can mitigate such misestimation.     

Impact of pre-treatment (soaking or germination) on nutrient and anti-nutrient contents,cooking time and acceptability of cooked red dry bean (Phaseolus vulgaris L.) and chickpea (Cicer arietinum L.) grown in Ethiopia

Pulses are processed in diverse ways prior to consumption. Soaking and germination are among the most common traditional, household-level food processing strategies. This study was carried out to determine the effects of soaking, germination, cooking and their combinations on the contents of selected nutrients and anti-nutrients of red dry bean and chickpea. In addition, the effects of pre-treatment on cooking time and the acceptability of dishes prepared from red dry bean and chickpea were determined. The nutrient compositions (zinc, iron and calcium) of most soaked-cooked and germinated-cooked red dry bean and chickpea samples were not significantly different than those of respective controls. However, soaking and germination pre-treatments significantly lowered the phytate and tannin contents of the red dry bean and chickpea samples, with a few exceptions, and overall, polyphenol contents were lower after soaking-cooking than after germination-cooking. Most scores for sensory attributes of bean-based and chickpea-based dishes prepared from soaked or germinated samples were not significantly different than those of the controls. For most red dry bean and chickpea samples, longer germination times yielded superior results in terms of reductions in cooking time, tannin content, and phytate:zinc and phytate:iron molar ratio.