Folding pentapeptides into left and right handed alpha helices

Left or right handed alpha helicity can be induced in a pentapeptide (ANGYG) by appending left or right handed helical cycles as chiral templates. This sequence corresponds to a rare left handed helix found in the protein alanine racemase. Circular dichroism spectra reveal that pentapeptide ANGYG has no detectable structure in aq phosphate buffer, that it is an ambidextrous peptide in that it can be directed to fold into either a left handed or right handed alpha helix in water, with greater propensity for the uncommon left handed than the normal right handed conformation. A helix-inducing cyclic peptide at both ends of this peptide was more effective at inducing alpha helicity than a single cyclic peptide at one end. The alpha helical cyclic peptides provide novel tools for folding short peptides into thermodynamically unstable helices in water, and for studying factors that control chirality and helix induction.     

Liquid-vapor phase diagram and cluster formation of two-dimensional ionic fluids

Direct molecular dynamics simulations on interfaces at constant temperature are performed to obtain the liquid-vapor phase diagram of the two-dimensional soft primitive model, an equimolar mixture of equal size spheres carrying opposite charges. Constant temperature and pressure simulations are also carried out to check consistency with interface simulations results. In addition, an analysis of the cluster formation of mixtures of particles with charge asymmetry in the range 1:1 to 1:36 at low and high densities is performed. The number of free ions, when plotted as a function of the positive ion charge, Z(+), has an oscillatory behavior and is independent of the density. The formation of aggregates is analyzed in terms of the attraction and repulsion between ions.     

A convenient one-pot synthesis of 1-aryl-substituted 2H-isoquinolin-3-ones

The synthesis of 1-aryl-substituted 2H-isoquinolin-3-ones is studied from 2-cyanomethylbenzoic acid and substituted benzenes via Friedel–Crafts acylation and intramolecular cyclization of 2-acylphenylacetonitriles formed in a one-pot method using sulfated zirconia as catalysts. Short reaction times, simplicity of operation, and easy work-up are some advantages of this method.     

Within the Ischemic Penumbra,Sub-Cellular Compartmentalization of Heat Shock Protein 70 Overlaps with Autophagy Proteins and Fails to Merge with Lysosomes

The brain area which surrounds the frankly ischemic region is named the area penumbra. In this area, most cells are spared although their oxidative metabolism is impaired. area penumbra is routinely detected by immunostaining of a molecule named Heat Shock Protein 70 (HSP70). Within the area penumbra, autophagy-related proteins also increase. Therefore, in the present study, the autophagy-related microtubule-associated protein I/II-Light Chain 3 (LC3) was investigated within the area penumbra along with HSP70. In C57 black mice, ischemia was induced by permanent occlusion of the distal part of the middle cerebral artery. Immunofluorescence and electron microscopy show that LC3 and HSP70 are overexpressed and co-localize within the area penumbra in the same cells and within similar subcellular compartments. In the area penumbra, marked loss of co-localization of HSP70 and LC3-positive autophagy vacuoles, with lysosomal-associated membrane protein 1 (LAMP1) or cathepsin-D-positive lysosome vacuoles occurs. This study indicates that, within the area penumbra, a failure of autophagolysosomes depends on defective compartmentalization of LC3, LAMP1 and cathepsin-D and a defect in merging between autophagosomes and lysosomes. Such a deleterious effect is likely to induce a depletion of autophagolysosomes and cell clearing systems, which needs to be rescued in the process of improving neuronal survival.     

Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides

Chemical probes for chromatin reader proteins are valuable tools for investigating epigenetic regulatory mechanisms and evaluating whether the target of interest holds therapeutic potential. Developing potent inhibitors for the plant homeodomain (PHD) family of methylation readers remains a difficult task due to the charged, shallow and extended nature of the histone binding site that precludes effective engagement of conventional small molecules. Herein, we describe the development of novel proximity-reactive cyclopeptide inhibitors for PHD3—a trimethyllysine reader domain of histone demethylase KDM5A. Guided by the PHD3–histone co-crystal structure, we designed a sidechain-to-sidechain linking strategy to improve peptide proteolytic stability whilst maintaining binding affinity. We have developed an operationally simple solid-phase macrocyclization pathway, capitalizing on the inherent reactivity of the dimethyllysine ε-amino group to generate scaffolds bearing charged tetraalkylammonium functionalities that effectively engage the shallow aromatic ‘groove’ of PHD3. Leveraging a surface-exposed lysine residue on PHD3 adjacent to the ligand binding site, cyclic peptides were rendered covalent through installation of an arylsulfonyl fluoride warhead. The resulting lysine-reactive cyclic peptides demonstrated rapid and efficient labeling of the PHD3 domain in HEK293T lysates, showcasing the feasibility of employing proximity-induced reactivity for covalent labeling of this challenging family of reader domains.

We describe the development of covalent cyclic peptide ligands which target a chromatin methylation reader domain using a proximity-reactive sulfonyl fluoride moiety.     

Key Distribution Patterns Using Tangent Circle Structures

The problem of key management in a communications network is of primary importance. A key distribution pattern is an incidence structure which provides a secure method of distributing keys in a large network reducing storage requirements. It is of interest to find explicit constructions for key distribution patterns. In O'Keefe [5–7], examples are shown using the finite circle geometries (Minkowski, Laguerre and inversive planes); in Quinn [12], examples are constructed from conics in finite projective and affine planes. In this paper, we construct some examples using the finite tangent-circle structures, introduced in Quattrocchi and Rinaldi [10] and we give a comparison of the storage requirements.     

Weakly Regular and Regular sets in Minkowski planes

A Regular (respectively Weakly Regular) set for an incidence structure Q is a set of points such that the identity is the only automorphism of Q which maps onto itself (respectively which fixes pointwise). In this work Weakly Regular and Regular sets in Minkowski planes are investigated.Work done within the activity of G.N.S.A.G.A. of C.N.R. and supported by 40 % grants of M.U.R.S.T.G.Rinaldi thanks Fondazione Francesco Severi and Banca Popolare dell'Etruria e del Lazio for the prize which allowed this research.     

Crystal and molecular structure of (+)-6,7∶8,9∶10,11-tri-O-isopropylidene-2,3-dideoxy-d-arabino-l-allo-undec-2-enono-1,4-lactone,C20H30O9

The crystal structure of the title lactone, C₂₀H₃₀O₉, a potential precursor of uncommon 11-carbon sugar derivatives, has been determined by single-crystal diffraction methods. The compound crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=15.581(3),b=14.047(2),c=9.888(2) Å, andZ=4. The structure was solved by direct methods and refined by full-matrix least-squares toR=0.054. The absolute configuration of the seven stereogenic carbon atoms was deduced as 4R, 5R, 6R, 7R, 8S, 9R, 10R, being (R)-(+)-glyceraldehyde its progenitor. An intramolecular O-HO hydrogen bond is present. Weak interaction C-HO links the molecules in sheets parallel to the (100) plane.     

Crystal and molecular structure of (−)-1,2-O-isopropylidene-3-O-methyl-7,8-dideoxy-β-l-glycero-d-gluco-non-7-enofuranurono-9,6-lactone,C13H18O7

The crystal structure of the title lactone, C₁₃H₁₈O₇, has been determined by single crystal diffraction methods. The compound crystallizes in the monoclinic space groupP2₁ witha=13.231(2),b=10.248(2),c=5.348(1) Å,=96.66(2)°, andZ=2. A total of 1055 reflection intensities were recorded on a Siemens AED single-crystal diffractometer (CuK radiation) at room temperature. The structure was solved by direct methods and electron density calculations. Full-matrix least-squares refinement gaveR=0.055 for 946 unique reflections above 2(I). The absolute configuration of the six chiral carbon atoms was deduced as 4S, 5R, 6R, 7S, 9R, 10R (crystallographic numbering corresponds to C-6, 5, 4, 3, 2, 1 in the title compound). An intermolecular O-HO hydrogen bond joins the molecules in chains which run along the twofold screw axis.