Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.     

Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS

Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein’s size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds.

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Evaluation of the geopolymer/nanofiber interfacial bond strength and their effects on Mode-I fracture toughness of geopolymer matrix at high temperature

The present article has reported the effects of several nanofiller’s aspect ratio, length and interfacial strength on Mode-I fracture toughness (K_IC) of geopolymer as the matrix of continuous fibre reinforced composites. These nanofillers have been chosen based on the variations in the surface chemistry and nature of interfacial bonding with geopolymer, which include Carbon, Alumina and Silicon carbide. Geopolymer matrix was subjected to the addition of single volume fraction, 2% of each type of nanofiller with two aspect ratios, designated as nanoparticles and nanofibers. Notched beam flexure tests (SEVNB) of neat and each nanofiller reinforced samples suggest that, while baseline K_IC of neat geopolymer improved with heat treatment, nanofibers with high interfacial bond strength showed maximum capability in further improving K_IC. Among those nanofibers, 2 vol% Silicon Carbide Whisker (SCW) showed the largest improvement in K_IC of geopolymer, which is ~164%. After heat treatment at 650 °C, SCW reinforcement was also found to be effective, with only ~28% lower than the reinforcing performance at 250 °C, while the performance of Alumina Nanofiber reinforced geopolymer notably reduced. SEM and EDS analysis suggested that the inhomogeneity in neat geopolymer and length of nanofibers control the reinforcing capability as well as crack propagation resistance of geopolymer. For instance, minimum length of nanofillers to toughen this geopolymer at 250 °C was required as ~2 μm. The results further suggested that the sample failure occurred due to the dominance of tensile failure of nanofibers over the interfacial separation.     

Novel mixed ligand coordination compounds of some rare earth metal cations containing acesulfamato/N,N-diethylnicotinamide

The mixed ligand coordination compounds containing acesulfamato and N,N -diethylnicotinamide biomolecules of some rare earth metal cations (Eu³⁺, Tb³⁺, Ho³⁺, Er³⁺ and Yb³⁺) were synthesized, and their structural properties were investigated. Possible structural formulas have been proposed by determining the chemical composition of molecules (elemental analysis), binding properties (infrared spectroscopy, mass analysis, solid-state UV-vis spectroscopy), thermal degradation properties (TGA / DTA curves). Based on the data collected, it is suggested that rare earth metal cations with a 3+ oxidation state have sextet coordination. The geometries of the structures were thought to be distorted octahedral. The charge balance of the coordination sphere is balanced by a monoanionic acesulfamato located outside the coordination sphere. When the thermal behaviours of the complexes were examined, it was determined that the compounds with Eu³⁺, Tb³⁺, and Yb³⁺ metal cations contained one hydrate water outside the coordination sphere. Hydrate waters do not exist in the Ho³⁺ and Er³⁺ metal cation-centred complexes. At the end of the thermal decomposition analysis of all complex structures, it was determined that they leave the relevant metal oxides in the reaction vessels as final decomposition products.     

Sequential feature‐based mesh movement and adjoint error‐based mesh refinement

Nowadays, aerodynamic computational modeling is carried out on a daily basis in an industrial setting. This is done with the aim of predicting the performance and flow characteristics of new components. However, limited resources in terms of time and hardware force the engineer to employ relatively coarse computational grids, thus achieving results with variable degree of inaccuracy. In this article, a novel combination of feature and adjoint‐based mesh adaptation methods is investigated and applied to typical three‐dimensional turbomachinery cases, such as compressor and fan blades. The proposed process starts by employing feature‐based mesh movement to improve the global flow solution and then adjoint refinement to tune the mesh for each quantity of interest. Comparison of this process with one utilizing only the adjoint refinement procedure shows significant benefits in terms of accuracy of the performance quantity.     

Deep Eutectic Solvents Based on Natural Ascorbic Acid Analogues and Choline Chloride

Deep eutectic solvents (DES) are one of the most promising green technologies to emerge in recent years given their combination of environmentally friendly credentials and useful functionalities. Considering the continued search for new DES – especially those that exemplify the aforementioned characteristics, we report the preparation of DES based on natural analogues of l -ascorbic acid for the first time. The onset of eutectic melting occurred at temperatures far below the melting point of the individual components and resulted in the generation of glass forming fluids with glass transition temperatures, viscosities and flow behavior that are comparable to similar systems. This work expands the current array of DES that can be produced using naturally occurring components, which given their potential to be bio-derived, interesting physicochemical properties (e. g. propensity to supercool and vitrify) and apparent antibacterial nature, may provide utility within a range of applications.     

Comparing Hydrogen Deuterium Exchange and Fast Photochemical Oxidation of Proteins: a Structural Characterisation of Wild-Type and ΔN6 β<Subscript>2</Subscript>-Microglobulin

Hydrogen deuterium exchange (HDX) coupled to mass spectrometry (MS) is a well-established technique employed in the field of structural MS to probe the solvent accessibility, dynamics and hydrogen bonding of backbone amides in proteins. By contrast, fast photochemical oxidation of proteins (FPOP) uses hydroxyl radicals, liberated from the photolysis of hydrogen peroxide, to covalently label solvent accessible amino acid side chains on the microsecond-millisecond timescale. Here, we use these two techniques to study the structural and dynamical differences between the protein β₂-microglobulin (β₂m) and its amyloidogenic truncation variant, ΔN6. We show that HDX and FPOP highlight structural/dynamical differences in regions of the proteins, localised to the region surrounding the N-terminal truncation. Further, we demonstrate that, with carefully optimised LC-MS conditions, FPOP data can probe solvent accessibility at the sub-amino acid level, and that these data can be interpreted meaningfully to gain more detailed understanding of the local environment and orientation of the side chains in protein structures.

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O→S Relay Deprotection: A General Approach to Controllable Donors of Reactive Sulfur Species

Reactive sulfur species (RSS) are biologically important molecules. Among them, H₂S, hydrogen polysulfides (H₂S_n, n>1), persulfides (RSSH), and HSNO are believed to play regulatory roles in sulfur‐related redox biology. However, these molecules are unstable and difficult to handle. Having access to their reliable and controllable precursors (or donors) is the prerequisite for the study of these sulfur species. Reported in this work is the preparation and evaluation of a series of O‐silyl‐mercaptan‐based sulfur‐containing molecules which undergo pH‐ or F^?‐mediated desilylation to release the corresponding H₂S, H₂S_n, RSSH, and HSNO in a controlled fashion. This O→S relay deprotection serves as a general strategy for the design of pH‐ or F^?‐triggered RSS donors. Moreover, we have demonstrated that the O‐silyl groups in the donors could be changed into other protecting groups like esters. This work should allow the development of RSS donors with other activation mechanisms (such as esterase‐activated donors).     

On the selective reduction of the distal olefin in geraniol and farnesol derivatives

The selective reduction of the distal olefin of many types of terpenoid-based natural products has been commonly approached using gaseous HCl in CH₂Cl₂. We herein present evidence that this method is inefficient and produces many side products, whose formation, in our hands, was difficult to avoid (over several reaction runs). A more efficient procedure for geranyl acetate using 1 equiv. of TiCl₄ in CH₂Cl₂ at −78°C is reported.     

Structure and reflective properties of Al-Cu-Fe quasicrystalline thin film prepared by laser induced arc method

Al-Cu-Fe thin films were prepared by laser induced arc (laser-arc) method from a single source-Al63Cu25Fe12 alloy, which was proved to consist of quasicrystalline phase together with approximant phase. The composition of the deposited films meets the requirement for formation of icosahedral symmetry phase. Quasicrystalline phase was obtained after annealing the amorphous as-deposit film samples. The optical properties of the samples were investigated. Thin film samples of Al, Cu and Fe deposited under the same condition were employed for comparison. The results showed specific reflective properties of Al-Cu-Fe quasicrystal thin film in some wavelength range. The optical conductivity of the films exhibited a negative peak, centered about 440 nm in range of 190to 800 nm. The Al-Cu-Fe quasicrystal thin films could absorb almost all the ray in the wavelength range from 420nm to 450 nm. The ratio of absorption was greater than 99%.