Investigation of Relationships between Grain Structure and Inhomogeneous Deformation by Means of Laboratory-Based Multimodal X-Ray Tomography: Strain Accuracy Analysis

Experimental Mechanics - The internal strain distribution developing during plastic deformation is important for understanding the mechanical properties of polycrystalline materials. Such...     

Sufficient Conditions for a Digraph to be Supereulerian

A (di)graph is supereulerian if it contains a spanning eulerian sub(di)graph. This property is a relaxation of hamiltonicity. Inspired by this analogy with hamiltonian cycles and by similar results in supereulerian graph theory, we analyze a number of sufficient Ore type conditions for a digraph to be supereulerian. Furthermore, we study the following conjecture due to Thomassé and the first author: if the arc‐connectivity of a digraph is not smaller than its independence number, then the digraph is supereulerian. As a support for this conjecture we prove it for digraphs that are semicomplete multipartite or quasitransitive and verify the analogous statement for undirected graphs.     

Azasugar inhibitors as pharmacological chaperones for Krabbe disease

Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe a new approach for the synthesis of galacto-configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure–activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease.     

The ABC of Insulin: The Organic Chemistry of a Small Protein

Insulin is a small protein crucial for regulating the blood glucose level in all animals. Since 1922 it has been used for the treatment of patients with diabetes. Despite consisting of just 51 amino acids, insulin contains 17 of the proteinogenic amino acids, A- and B-chains, three disulfide bridges, and it folds with 3 α-helices and a short β-sheet segment. Insulin associates into dimers and further into hexamers with stabilization by Zn²⁺ and phenolic ligands. Selective chemical modification of proteins is at the forefront of developments in chemical biology and biopharmaceuticals. Insulin's structure has made it amenable to organic and inorganic chemical reactions. This Review provides a synthetic organic chemistry perspective on this small protein. It gives an overview of key chemical and physico-chemical aspects of the insulin molecule, with a focus on chemoselective reactions. This includes N-acylations at the N-termini or at Lys^B29 by pH control, introduction of protecting groups on insulin, binding of metal ions, ligands to control the nano-scale assembly of insulin, and more.     

DIY XES—development of an inexpensive,versatile, and easy to fabricate XES analyzer and sample delivery system

The application of X-ray emission spectroscopy (XES) has grown substantially with the development of X-ray free-electron lasers, third and fourth generation synchrotron sources, and high-power benchtop sources. By providing the high X-ray flux required for XES, these sources broaden the availability and application of this method of probing electronic structure. As the number of sources increase, so does the demand for X-ray emission detection and sample delivery systems that are cost effective and customizable. Here, we present a detailed fabrication protocol for von Hamos X-ray optics and give details for a 3D-printed spectrometer design. Additionally, we outline an automated, externally triggered liquid sample delivery system that can be used to repeatedly deliver nanoliter droplets onto a plastic substrate for measurement. These systems are both low cost, efficient, and easy to recreate or modify depending on the application. A low cost multiple X-ray analyzer system enables measurement of dilute samples, whereas the sample delivery limits sample loss and reproducibly replaces spent sample with fresh sample in the same position. While both systems can be used in a wide range of applications, the design addresses several challenges associated specifically with time-resolved XES (TRXES). As an example application, we show results from TRXES measurements of photosystem II, a dilute, photoactive protein.     

Separation of cannabinoids on three different mixed‐mode columns containing carbon/nanodiamond/amine‐polymer superficially porous particles

Three mixed‐mode high‐performance liquid chromatography columns packed with superficially porous carbon/nanodiamond/amine‐polymer particles were used to separate mixtures of cannabinoids. Columns evaluated included: (i) reversed phase (C₁₈), weak anion exchange, 4.6 × 33 mm, 3.6 μm, and 4.6 × 100 mm, 3.6 μm, (ii) reversed phase, strong anion exchange (quaternary amine), 4.6×33 mm, 3.6 μm, and (iii) hydrophilic interaction liquid chromatography, 4.6 × 150 mm, 3.6 μm. Different selectivities were achieved under various mobile phase and stationary phase conditions. Efficiencies and peak capacities were as high as 54 000 N/m and 56, respectively. The reversed phase mixed‐mode column (C₁₈) retained tetrahydrocannabinolic acid strongly under acidic conditions and weakly under basic conditions. Tetrahydrocannabinolic acid was retained strongly on the reversed phase, strong anion exchange mixed‐mode column under basic polar organic mobile phase conditions. The hydrophilic interaction liquid chromatography column retained polar cannabinoids better than the (more) neutral ones under basic conditions. A longer reversed phase (C₁₈) mixed‐mode column (4.6 × 100 mm) showed better resolution for analytes (and a contaminant) than a shorter column. Fast separations were achieved in less than 5 min and sometimes 2 min. A real world sample (bubble hash extract) was also analyzed by gradient elution.     

Disjoint Paths in Decomposable Digraphs

The k‐linkage problem is as follows: given a digraph and a collection of k terminal pairs such that all these vertices are distinct; decide whether D has a collection of vertex disjoint paths such that is from to for . A digraph is k‐linked if it has a k‐linkage for every choice of 2k distinct vertices and every choice of k pairs as above. The k‐linkage problem is NP‐complete already for [11] and there exists no function such that every ‐strong digraph has a k‐linkage for every choice of 2k distinct vertices of D [17]. Recently, Chudnovsky et al. [9] gave a polynomial algorithm for the k‐linkage problem for any fixed k in (a generalization of) semicomplete multipartite digraphs. In this article, we use their result as well as the classical polynomial algorithm for the case of acyclic digraphs by Fortune et al. [11] to develop polynomial algorithms for the k‐linkage problem in locally semicomplete digraphs and several classes of decomposable digraphs, including quasi‐transitive digraphs and directed cographs. We also prove that the necessary condition of being ‐strong is also sufficient for round‐decomposable digraphs to be k‐linked, obtaining thus a best possible bound that improves a previous one of . Finally we settle a conjecture from [3] by proving that every 5‐strong locally semicomplete digraph is 2‐linked. This bound is also best possible (already for tournaments) [1].     

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.