The two new tetra­kis-substituted pyrazines, 1,1',1'',1'''-(pyrazine-2,3,5,6-tetra­yl) tetra­kis­(N,N-di­methyl­methanamine), C16H32N6, (I) and N,N',N'',N'''-[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene)]tetra­kis­(N-methyl­aniline), C36H40N6, (II), both crystallize with half a mol­ecule in the asymmetric unit; the whole mol­ecules are generated by inversion symmetry. There are weak intra­molecular C—H⋯N hydrogen bonds present in both mol­ecules and in (II) the pendant N-methyl­aniline rings are linked by a C—H⋯π inter­action. The degredation product, N,N'-[(6-phenyl-6,7-di­hydro-5H-pyrrolo­[3,4-b]pyrazine-2,3-di­yl)bis(methyl­ene)]bis­(N-methyl­aniline), C28H29N5, (III), was obtained several times by reacting (II) with different metal salts. Here, the 6-phenyl ring is almost coplanar with the planar pyrrolo­[3,4-b]pyrazine unit (r.m.s. deviation = 0.029 Å), with a dihedral angle of 4.41 (10)° between them. The two N-meth­yl­aniline rings are inclined to the planar pyrrolo­[3,4-b]pyrazine unit by 88.26 (10) and 89.71 (10)°, and to each other by 72.56 (13)°. There are also weak intra­molecular C—H⋯N hydrogen bonds present involving the pyrazine ring and the two N-methyl­aniline groups. In the crystal of (I), there are no significant inter­molecular contacts present, while in (II) mol­ecules are linked by a pair of C—H⋯π inter­actions, forming chains along the c-axis direction. In the crystal of (III), mol­ecules are linked by two pairs of C—H⋯π inter­actions, forming inversion dimers, which in turn are linked by offset π–π inter­actions [inter­centroid distance = 3.8492 (19) Å], forming ribbons along the b-axis direction.

Two polymorphs of the title compound, C19H16N2O3, were obtained from ethano­lic (polymorph I) and methano­lic solutions (polymorph II), respectively. Both polymorphs crystallize in the monoclinic system with four formula units per cell and a complete mol­ecule in the asymmetric unit. The main difference between the mol­ecules of (I) and (II) is the reversed position of the hy­droxy group of the carb­oxy­lic function. All other conformational features are found to be similar in the two mol­ecules. The different orientation of the OH group results in different hydrogen-bonding schemes in the crystal structures of (I) and (II). Whereas in (I) inter­molecular O—H⋯O hydrogen bonds with the pyridazinone carbonyl O atom as acceptor generate chains with a C(7) motif extending parallel to the b-axis direction, in the crystal of (II) pairs of inversion-related O—H⋯O hydrogen bonds with an R22(8) ring motif between two carb­oxy­lic functions are found. The inter­molecular inter­actions in both crystal structures were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

The asymmetric units of the title compounds, namely, catena-poly[[(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4N1,N4,N8,N11)nickel(II)]-μ-1,3-bis­(3-carboxyl­ato­prop­yl)tetra­methyl­disiloxane-κ2O:O'], [Ni(C10H24O5Si2)(C12H24N4)]n (I), and catena-poly[[[(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4N1,N4,N8,N11)nickel(II)]-μ-4-({[(3-carb­oxy­prop­yl)di­methyl­sil­yl]­oxy}di­methyl­sil­yl)butano­ato-κ2O:O'] per­chlorate], {[Ni(C10H25O5Si2)(C12H24N4)]ClO4}n (II), consist of one (in I) or two crystallographically non-equivalent (in II) centrosymmetric macrocyclic cations and one centrosymmetric dianion (in I) or two centrosymmetric monoanions (in II). In each compound, the metal ion is coordinated by the four secondary N atoms of the macrocyclic ligand, which adopts the most energetically stable trans-III conformation, and the mutually trans O atoms of the carboxyl­ate in a slightly tetra­gonally distorted trans-NiN4O2 octa­hedral coordination geometry. The crystals of both types of compounds are composed of parallel polymeric chains of the macrocyclic cations linked by the anions of the acid running along the [101] and [110] directions in I and II, respectively. In I, each polymeric chain is linked to four neighbouring ones by hydrogen bonding between the NH groups of the macrocycle and the carboxyl­ate O atoms, thus forming a three-dimensional supra­molecular network. In II, each polymeric chain contacts with only two neighbours, forming hydrogen bonds between the partially protonated carb­oxy­lic groups of the bridging ligand. As a result, a lamellar structure is formed with the layers oriented parallel to the (1overline{1}1) plane.

The title compounds, 5-(2H-1,3-benzodioxol-5-yl)-N-cyclo­hexyl­penta-2,4-dienamide, C18H21NO3 (I), and 5-(2H-1,3-benzodioxol-5-yl)-1-(pyrrolidin-1-yl)penta-2,4-dien-1-one C16H17NO3 (II), are derivatives of piperine, which is known as a pungent component of pepper. Their geometrical parameters are similar to those of the three polymorphs of piperine, which indicate conjugation of electrons over the length of the mol­ecules. The extended structure of (I) features N—H⋯O amide hydrogen bonds, which generate C(4) [010] chains. The crystal of (II) features aromatic π–π stacking, as for two of three known piperine polymorphs.

CsCl-type materials have many outstanding characteristics, i.e. simple in structure, ease of synthesis and good stability at room temperature, thus are an excellent choice for designing functional materials. Using high-throughput first-principles calculations, a large number of topological semimetals/metals (TMs) were designed from CsCl-type materials found in crystallographic databases and their crystal and electronic structures have been studied. The CsCl-type TMs in this work show rich topological character, ranging from triple nodal points, type-I nodal lines and critical-type nodal lines, to hybrid nodal lines. The TMs identified show clean topological band structures near the Fermi level, which are suitable for experimental investigations and future applications. This work provides a rich data set of TMs with a CsCl-type structure.

Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54–Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine–glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.

Malaria is a devastating disease caused by a protozoan parasite. It affects over 300 million individuals and results in over 400 000 deaths annually, most of whom are young children under the age of five. Hexokinase, the first enzyme in glucose metabolism, plays an important role in the infection process and represents a promising target for therapeutic intervention. Here, cryo-EM structures of two conformational states of Plasmodium vivax hexokinase (PvHK) are reported at resolutions of ∼3 Å. It is shown that unlike other known hexokinase structures, PvHK displays a unique tetrameric organization (∼220 kDa) that can exist in either open or closed quaternary conformational states. Despite the resemblance of the active site of PvHK to its mammalian counterparts, this tetrameric organization is distinct from that of human hexokinases, providing a foundation for the structure-guided design of parasite-selective antimalarial drugs.

p-Hydroxymandelate oxidase (Hmo) is a flavin mononucleotide (FMN)-dependent enzyme that oxidizes mandelate to benzoylformate. How the FMN-dependent oxidation is executed by Hmo remains unclear at the molecular level. A continuum of snapshots from crystal structures of Hmo and its mutants in complex with physiological/nonphysiological substrates, products and inhibitors provides a rationale for its substrate enantioselectivity/promiscuity, its active-site geometry/reactivity and its direct hydride-transfer mechanism. A single mutant, Y128F, that extends the two-electron oxidation reaction to a four-electron oxidative decarboxylation reaction was unexpectedly observed. Biochemical and structural approaches, including biochemistry, kinetics, stable isotope labeling and X-ray crystallo­graphy, were exploited to reach these conclusions and provide additional insights.

The Y128F single mutant of p-hydroxymandelate oxidase (Hmo) is capable of oxidizing mandelate to benzoate via a four-electron oxidative decarboxylation reaction. When benzoylformate (the product of the first two-electron oxidation) and hydrogen peroxide (an oxidant) were used as substrates the reaction did not proceed, suggesting that free hydrogen peroxide is not the committed oxidant in the second two-electron oxidation. How the flavin mononucleotide (FMN)-dependent four-electron oxidation reaction takes place remains elusive. Structural and biochemical explorations have shed new light on this issue. 15 high-resolution crystal structures of Hmo and its mutants liganded with or without a substrate reveal that oxidized FMN (FMNox) possesses a previously unknown electrophilic/nucleophilic duality. In the Y128F mutant the active-site perturbation ensemble facilitates the polarization of FMNox to a nucleophilic ylide, which is in a position to act on an α-ketoacid, forming an N5-acyl-FMNred dead-end adduct. In four-electron oxidation, an intramolecular disproportion­ation reaction via an N5-alkanol-FMNred C'α carbanion intermediate may account for the ThDP/PLP/NADPH-independent oxidative decarboxylation reaction. A synthetic 5-deaza-FMNox cofactor in combination with an α-hydroxyamide or α-ketoamide biochemically and structurally supports the proposed mechanism.

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Where the lack of a suitable homologue precludes conventional MR, one option is to predict the target structure using bioinformatics. Such modelling, in the absence of homologous templates, is called ab initio or de novo modelling. Recently, the accuracy of such models has improved significantly as a result of the availability, in many cases, of residue-contact predictions derived from evolutionary covariance analysis. Covariance-assisted ab initio models representing structurally uncharacterized Pfam families are now available on a large scale in databases, potentially representing a valuable and easily accessible supplement to the PDB as a source of search models. Here, the unconventional MR pipeline AMPLE is employed to explore the value of structure predictions in the GREMLIN and PconsFam databases. It was tested whether these deposited predictions, processed in various ways, could solve the structures of PDB entries that were subsequently deposited. The results were encouraging: nine of 27 GREMLIN cases were solved, covering target lengths of 109–355 residues and a resolution range of 1.4–2.9 Å, and with target–model shared sequence identity as low as 20%. The cluster-and-truncate approach in AMPLE proved to be essential for most successes. For the overall lower quality structure predictions in the PconsFam database, remodelling with Rosetta within the AMPLE pipeline proved to be the best approach, generating ensemble search models from single-structure deposits. Finally, it is shown that the AMPLE-obtained search models deriving from GREMLIN deposits are of sufficiently high quality to be selected by the sequence-independent MR pipeline SIMBAD. Overall, the results help to point the way towards the optimal use of the expanding databases of ab initio structure predictions.

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.

The Advanced Photon Source 1-ID beamline, operating in the 40–140 keV X-ray energy range, has successfully employed continuously tunable saw-tooth refractive lenses to routinely deliver beams focused in both one and two dimensions to experiments for over 15 years. The practical experience of implementing such lenses, made of silicon and aluminium, is presented, including their properties, control, alignment, and diagnostic methods, achieving ∼1 µm focusing (vertically). Ongoing development and prospects towards submicrometre focusing at these high energies are also mentioned.

New fitting analyses of two-dimensional diffraction-spot shapes are demonstrated to evaluate strain, strain distribution and domain size in a crystalline ultra-thin film. The evaluations are displayed as residual and population maps as a function of strain or domain size.

There are several hypotheses about how amphibian chytrid has spread around the world, but the trade in amphibians for food, bait, pets and laboratory animals has been identified as the most likely mode of spread

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The 5.8-magnitude earthquake that shook the eastern United States on the afternoon of Tuesday, Aug. 23, caused minor damage to some of the Smithsonian's natural history collections. All public Smithsonian museums are open and have been determined safe for visitors and staff.

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Paleontologists studying an extreme short-term global warming event have discovered direct evidence about how mammals respond to rising temperatures. In a study that appeared recently […]

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A newly described species of toothed whale that lived some 3-4 million years ago during the Pliocene, is causing scientists to reconsider what is known about its living cold-water relatives: narwhals and belugas.

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A new study finds that since 1985, half of Australia's Great Barrier Reef coral has died.

The post Smithsonian marine biologist Nancy Knowlton discusses Great Barrier Reef coral dieoff on PBS NewsHour appeared first on Smithsonian Insider.

Using echolocation alone the bats found, identified and captured insects perched motionless and silent on the leaves of plants.

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Save the Rhinos! Save the Elephants! Save the humans?! It seems strange to be connecting our own fate to that of wildlife but new research […]

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The carabid beetle tribe Lachnophorini is the focus of an extensive new study by two Smithsonian entomologists just published in a special issue of the […]

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In theory, crabs of the species Planes major should stay true to their mates for life. Heterosexual pairs of these small crustaceans live on loggerhead […]

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One hundred years after the extinction of the passenger pigeon, the nation’s top bird science and conservation groups have come together to publish The State […]

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When some of the world’s largest mammals come your way, most animals steer clear. Not the genet. The small cat-like carnivore was captured on film […]

The post Maybe it’s safer riding a rhino. Genet expert poses new ideas on the mammal’s hitchhiking behavior appeared first on Smithsonian Insider.

Skygazers at northern latitudes are familiar with the W-shaped star pattern of Cassiopeia the Queen. This circumpolar constellation is visible year-round near the North Star. […]

The post CASSIOPEIA’S HIDDEN GEM: THE CLOSEST ROCKY, TRANSITING PLANET appeared first on Smithsonian Insider.

We only have one example of a planet with life: Earth. But within the next generation, it should become possible to detect signs of life […]

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Four years after conservationists relocated 570 desert tortoises (Gopherus agassizii) in California from a threatened habitat to a new nearby location, the tortoises outwardly appeared […]

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Hundreds of experiments have shown biodiversity fosters healthier, more productive ecosystems. But many experts doubted whether these experiments would hold up in the real world. […]

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Death-associated protein kinase 1 (DAPK1) is a serine/threonine protein kinase that regulates apoptosis and autophagy. DAPK1 is considered to be a therapeutic target for amyloid-β deposition, endometrial adenocarcinomas and acute ischemic stroke. Here, the potent inhibitory activity of the natural anthraquinone purpurin against DAPK1 phosphorylation is shown. Thermodynamic analysis revealed that while the binding affinity of purpurin is similar to that of CPR005231, which is a DAPK1 inhibitor with an imidazopyridazine moiety, the binding of purpurin was more enthalpically favorable. In addition, the inhibition potencies were correlated with the enthalpic changes but not with the binding affinities. Crystallographic analysis of the DAPK1–purpurin complex revealed that the formation of a hydrogen-bond network is likely to contribute to the favorable enthalpic changes and that stabilization of the glycine-rich loop may cause less favorable entropic changes. The present findings indicate that purpurin may be a good lead compound for the discovery of inhibitors of DAPK1, and the observation of enthalpic changes could provide important clues for drug development.

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

Osiris Martinez-Guzman, Mathilda M. Willoughby, Arushi Saini, Jonathan V. Dietz, Iryna Bohovych, Amy E. Medlock, Oleh Khalimonchuk, and Amit R. Reddi

Heme is a cofactor and signaling molecule that is essential for much of aerobic life. All heme-dependent processes in eukaryotes require that heme is trafficked from its site of synthesis in the mitochondria to hemoproteins located throughout the cell. However, the mechanisms governing the mobilization of heme out of the mitochondria, and the spatio-temporal dynamics of these processes, are poorly understood. Herein, using genetically encoded fluorescent heme sensors, we developed a live cell assay to monitor heme distribution dynamics between the mitochondrial inner-membrane, where heme is synthesized, and the mitochondrial matrix, cytosol, and nucleus. Surprisingly, heme trafficking to the nucleus is ~25% faster than to the cytosol or mitochondrial matrix, which are nearly identical, potentially supporting a role for heme as a mitochondrial-nuclear retrograde signal. Moreover, we discovered that the heme synthetic enzyme, 5-aminolevulinic acid synthase (ALAS), and GTPases in control of the mitochondrial dynamics machinery, Mgm1 and Dnm1, and ER contact sites, Gem1, regulate the flow of heme between the mitochondria and nucleus. Overall, our results indicate that there are parallel pathways for the distribution of bioavailable heme.

Tara L. Mastro, Vishnu P. Tripathi, and Susan L. Forsburg

Translesion synthesis polymerases (TLSPs) are non-essential error-prone enzymes that ensure cell survival by facilitating DNA replication in the presence of DNA damage. In addition to their role in bypassing lesions, TLSPs have been implicated in meiotic double strand break repair in several systems. Here we examine the joint contribution of four TLS polymerases to meiotic progression in the fission yeast S. pombe. We observed the dramatic loss of spore viability in fission yeast lacking all four TLSPs which is accompanied by disruptions in chromosome segregation during meiosis I and II. Rec8 cohesin dynamics are altered in the absence of the TLSPs. These data suggest that the TLSPs contribute to multiple aspects of meiotic chromosome dynamics.

Have an upset stomach? Pop a chalky, chewable antacid. Maybe you’ve got a painful cut or burn. No problem; reach for a healing ointment or […]

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The Pan-STARRS project at the University of Hawai’i Institute for Astronomy (UH IfA) is publicly releasing the world’s largest digital sky survey today from the […]

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A hunter touches an infected animal’s blood, a farmer breathes the moist air exhaled by sick cows, contaminated meat is served at an outdoor market—these […]

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The use of strongly bent crystals in spectrometers for pulses of a hard X-ray free-electron laser is explored theoretically. Diffraction is calculated in both dynamical and kinematical theories. It is shown that diffraction can be treated kinematically when the bending radius is small compared with the critical radius given by the ratio of the Bragg-case extinction length for the actual reflection to the Darwin width of this reflection. As a result, the spectral resolution is limited by the crystal thickness, rather than the extinction length, and can become better than the resolution of a planar dynamically diffracting crystal. As an example, it is demonstrated that spectra of the 12 keV pulses can be resolved in the 440 reflection from a 20 µm-thick diamond crystal bent to a radius of 10 cm.

Entangled embedded periodic nets and crystal frameworks are defined, along with their dimension type, homogeneity type, adjacency depth and periodic isotopy type. Periodic isotopy classifications are obtained for various families of embedded nets with small quotient graphs. The 25 periodic isotopy classes of depth-1 embedded nets with a single-vertex quotient graph are enumerated. Additionally, a classification is given of embeddings of n-fold copies of pcu with all connected components in a parallel orientation and n vertices in a repeat unit, as well as demonstrations of their maximal symmetry periodic isotopes. The methodology of linear graph knots on the flat 3-torus [0,1)3 is introduced. These graph knots, with linear edges, are spatial embeddings of the labelled quotient graphs of an embedded net which are associated with its periodicity bases.

Researchers at the Smithsonian's National Zoo's new genetics lab use animal DNA to diagnose new diseases, discover new species help in conservation efforts and solve mysteries.

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What does it take to care for a pride of lions? Go behind the scenes with Great Cats Curator Craig Saffoe as he works with animal keepers and veterinarians to prepare the National Zoo's frisky lion cubs for their public debut. For more about the Zoo's growing pride and to watch them on live webcams: http://nationalzoo.si.edu/Animals/GreatCats/default.cfm?cam=LC4

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The post Roland Kays, curator of mammals at the New York State Museum, discusses a new Smithsonian Website for sharing camera-trap images of wild animals appeared first on Smithsonian Insider.

The post Smithsonian geologist Liz Cottrell discusses the March 11, 2011 Japan earthquake and its mechanics appeared first on Smithsonian Insider.

Tom Crouch, Senior curator in the National Air and Space Museum's Aeronautics Division, discusses Thaddeus Lowe and the birth of American aerial reconnaissance during the Civil War. This presentation was recorded on May 11, 2011 on the National Mall.

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Kari Bruwelheide, forensic anthropologist at the Smithsonian's National Museum of Natural History, discusses how she came to work at the museum, the power of human remains and the information that bones can contain. She and her colleagues continue to discover new ways to interpret evidence from bones and burials.

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The post Museum Conservation Institute research scientist Ed Vicenzi discusses his work analyzing daguerreotypes appeared first on Smithsonian Insider.

Maintaining natural movement of animals that live in the tropical rainforest canopy in South America is important for the health of the ecosystem. As development […]

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Judy Garland’s iconic ruby slippers from “The Wizard of Oz” are one of the most popular attractions at the National Museum of American History. But […]

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The circus is coming to the Smithsonian! The Big Top went up on the National Mall this week in preparation for the 2017 Smithsonian Folklife […]

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