A study on chiral monomolecular compound structures found in the Cambridge Structural Database is presented.

The crystal structure of malayaite, CaSnOSiO4, at T = 20 K has been refined, based on the presence of satellite reflections with a modulation vector of 0.26b*. The structural modulation is attributed to a soft optic phonon, dominated by motion of the Ca atoms.

The solvent-mediated desolvation process of newly discovered lenvatinib DMSO solvate to form II at different water volume fractions and temperatures was investigated. It is confirmed that the activity of water is the most important factor affecting the desolvation process: the desolvation process only occurs when the activity of water is greater than the activity of DMSO, and one new mechanism of solvent-mediated desolvation process was proposed.

The crystal structure of the nanocrystalline pigment mono­methyl-quinacridone was solved from X-ray powder data. The orientational disorder was investigated using Rietveld refinements, structure refinement to the pair-distribution function, and lattice-energy minimizations of various ordered structural models.

The synthesis, characterization and study of structures from a series of bi­phenyls substituted at positions 3, 3', 4 and 4' with groups connected to the bi­phenyl core through oxygen atoms are presented here. The molecular conformation is extensively studied both in the solid as well as in the liquid state, and the effect of different actors (such as packing and chain length) on the torsion angle between aromatic rings is analyzed.

Crystal structure and microscopic optical properties of anthracene derivative compounds have been investigated by single-crystal synchrotron X-ray diffraction, laser confocal microscopy and fluorescence lifetime imaging microscopy.

A single-chain, tailless Xenopus laevis H2A/H2B dimer construct (scH2BH2A) was engineered by directly fusing the C-terminus of H2B to the N-terminus of H2A without an artificial linker sequence. A high-resolution crystal structure of scH2BH2A shows that it adopts a nearly identical fold to that of nucleosomal H2A/H2B and may be useful for future structural studies of many H2A/H2B-interacting proteins.

Insights were obtained into the structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway for the biosynthesis of lysine.

The crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum is reported. It has high structural similarity to other gluconate 5-dehydrogenase proteins, demonstrating that this enzyme is highly conserved.

The crystal structure of Pseudomonas aeruginosa Fis is composed of an N-terminal flexible loop and a C-terminal helix–turn–helix motif.

This article reports conformational polymorphisms of the EF-hand protein MCFD2 which is involved in glycoprotein transport..

The structure of the Pseudomonas aeruginosa T6SS PldB immunity protein PA5086 is reported at 1.9 Å resolution. Comparison of PA5086 with its homologs PA5087 and PA5088 showed great similarities in sequence and structure, but vast divergences in electrostatic potential surfaces.

Aerobic thermoacidophilic archaea belonging to the genus Sulfolobus harbor peroxiredoxins, thiol-dependent peroxidases that assist in protecting the cells from oxidative damage. Here, the crystal structure of the 1-Cys peroxiredoxin from Sulfolobus islandicus, named 1-Cys SiPrx, is presented. A 2.75 Å resolution data set was collected from a crystal belonging to space group P212121, with unit-cell parameters a = 86.8, b = 159.1, c = 189.3 Å, α = β = γ = 90°. The structure was solved by molecular replacement using the homologous Aeropyrum pernix peroxiredoxin (ApPrx) structure as a search model. In the crystal structure, 1-Cys SiPrx assembles into a ring-shaped decamer composed of five homodimers. This quaternary structure corresponds to the oligomeric state of the protein in solution, as observed by size-exclusion chromatography. 1-Cys SiPrx harbors only a single cysteine, which is the peroxidatic cysteine, and lacks both of the cysteines that are highly conserved in the C-terminal arm domain in other archaeal Prx6-subfamily proteins such as ApPrx and that are involved in the association of dimers into higher-molecular-weight decamers and dodecamers. It is thus concluded that the Sulfolobus Prx6-subfamily protein undergoes decamerization independently of arm-domain cysteines.

The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality-control pathway in eukaryotes in which misfolded ER proteins are polyubiquitylated, extracted and ultimately degraded by the proteasome. This process involves ER membrane-embedded ubiquitin E2 and E3 enzymes, as well as a soluble E2 enzyme (Ubc7 in Saccharomyces cerevisiae and UBE2G2 in mammals). E2-binding regions (E2BRs) that recruit these soluble ERAD E2s to the ER have been identified in humans and S. cerevisiae, and structures of E2–E2BR complexes from both species have been determined. In addition to sequence and structural differences between the human and S. cerevisiae E2BRs, the binding of E2BRs also elicits different biochemical outcomes with respect to E2 charging by E1 and E2 discharge. Here, the Schizosaccharomyces pombe E2BR was identified and purified with Ubc7 to resolve a 1.7 Å resolution co-crystal structure of the E2BR in complex with Ubc7. The S. pombe E2BR binds to the back side of the E2 as an α-helix and, while differences exist, it exhibits greater similarity to the human E2BR. Structure-based sequence alignments reveal differences and conserved elements among these species. Structural comparisons and biochemistry reveal that the S. pombe E2BR presents a steric impediment to E1 binding and inhibits E1-mediated charging, respectively.

A putative open reading frame encoding GTP cyclohydrolase I from Listeria monocytogenes was expressed in a recombinant Escherichia coli strain. The recombinant protein was purified and was confirmed to convert GTP to dihydroneopterin triphosphate (Km = 53 µM; vmax = 180 nmol mg−1 min−1). The protein was crystallized from 1.3 M sodium citrate pH 7.3 and the crystal structure was solved at a resolution of 2.4 Å (Rfree = 0.226) by molecular replacement using human GTP cyclohydrolase I as a template. The protein is a D5-symmetric decamer with ten topologically equivalent active sites. Screening a small library of about 9000 compounds afforded several inhibitors with IC50 values in the low-micromolar range. Several inhibitors had significant selectivity with regard to human GTP cyclohydrolase I. Hence, GTP cyclohydrolase I may be a potential target for novel drugs directed at microbial infections, including listeriosis, a rare disease with high mortality.

Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.

The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipo­amide succinyltransferase isolated without an expression tag and in this novel crystal form.

The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U–U mismatch sandwiched between Watson–Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U–C/C–U) mismatches flanked by U–G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.

The membrane protein EsaA is a conserved component of the type VIIb secretion system. Limited proteolysis of purified EsaA from Staphylococcus aureus USA300 identified a stable 48 kDa fragment, which was mapped by fingerprint mass spectrometry to an uncharacterized extracellular segment of EsaA. Analysis by circular dichroism spectroscopy showed that this fragment folds into a single stable domain made of mostly α-helices with a melting point of 34.5°C. Size-exclusion chromatography combined with multi-angle light scattering indicated the formation of a dimer of the purified extracellular domain. Octahedral crystals were grown in 0.2 M ammonium citrate tribasic pH 7.0, 16% PEG 3350 using the hanging-drop vapor-diffusion method. Diffraction data were analyzed to 4.0 Å resolution, showing that the crystals belonged to the enantiomorphic tetragonal space groups P41212 or P43212, with unit-cell parameters a = 197.5, b = 197.5, c = 368.3 Å, α = β = γ = 90°.

This study presents the crystal structure of a thiol variant of the human mitochondrial branched-chain aminotransferase protein. Human branched-chain aminotransferase (hBCAT) catalyzes the transamination of the branched-chain amino acids leucine, valine and isoleucine and α-ketoglutarate to their respective α-keto acids and glutamate. hBCAT activity is regulated by a CXXC center located approximately 10 Å from the active site. This redox-active center facilitates recycling between the reduced and oxidized states, representing hBCAT in its active and inactive forms, respectively. Site-directed mutagenesis of the redox sensor (Cys315) results in a significant loss of activity, with no loss of activity reported on the mutation of the resolving cysteine (Cys318), which allows the reversible formation of a disulfide bond between Cys315 and Cys318. The crystal structure of the oxidized form of the C318A variant was used to better understand the contributions of the individual cysteines and their oxidation states. The structure reveals the modified CXXC center in a conformation similar to that in the oxidized wild type, supporting the notion that its regulatory mechanism depends on switching the Cys315 side chain between active and inactive conformations. Moreover, the structure reveals conformational differences in the N-terminal and inter-domain region that may correlate with the inactivated state of the CXXC center.

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.

Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP–4 complex indicated close similarities in the protein–ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.

Immunoglobulin E (IgE) plays a central role in the allergic response, in which cross-linking of allergen by Fc∊RI-bound IgE triggers mast cell and basophil degranulation and the release of inflammatory mediators. The high-affinity interaction between IgE and Fc∊RI is a long-standing target for therapeutic intervention in allergic disease. Omalizumab is a clinically approved anti-IgE monoclonal antibody that binds to free IgE, also with high affinity, preventing its interaction with Fc∊RI. All attempts to crystallize the pre-formed complex between the omalizumab Fab and the Fc region of IgE (IgE-Fc), to understand the structural basis for its mechanism of action, surprisingly failed. Instead, the Fab alone selectively crystallized in different crystal forms, but their structures revealed intermolecular Fab/Fab interactions that were clearly strong enough to disrupt the Fab/IgE-Fc complexes. Some of these interactions were common to other Fab crystal structures. Mutations were therefore designed to disrupt two recurring packing interactions observed in the omalizumab Fab crystal structures without interfering with the ability of the omalizumab Fab to recognize IgE-Fc; this led to the successful crystallization and subsequent structure determination of the Fab/IgE-Fc complex. The mutagenesis strategy adopted to achieve this result is applicable to other intractable Fab/antigen complexes or systems in which Fabs are used as crystallization chaperones.

Mycobacterium tuberculosis produces glycogen (also known as α-glucan) to help evade human immunity. This pathogen uses the GlgE pathway to generate glycogen rather than the more well known glycogen synthase GlgA pathway, which is absent in this bacterium. Thus, the building block for this glucose polymer is α-maltose-1-phosphate rather than an NDP-glucose donor. One of the routes to α-maltose-1-phosphate is now known to involve the GlgA homologue GlgM, which uses ADP-glucose as a donor and α-glucose-1-phosphate as an acceptor. To help compare GlgA (a GT5 family member) with GlgM enzymes (GT4 family members), the X-ray crystal structure of GlgM from Mycobacterium smegmatis was solved to 1.9 Å resolution. While the enzymes shared a GT-B fold and several residues responsible for binding the donor substrate, they differed in some secondary-structural details, particularly in the N-terminal domain, which would be expected to be largely responsible for their different acceptor-substrate specificities.

A recent study of dog bones excavated from archaeological sites on the Channel Islands of California has cast new light on the past ecology of the islands and the impact that domestic dogs--brought to the islands by Native Americans more than 6,000 years ago—may have once had on the islands’ animals and ecosystems.

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The Smithsonian Tropical Research Institute in Panama was recently given a collection of more than 25,000 different pollen grains and spores, each mounted on a microscope slide and labeled according to the plant that produced it. “The collection is worldwide in coverage with an emphasis on plants of the Americas,” explains collection donor Alan Graham, professor emeritus at Kent State University and curator at the Missouri Botanical Garden.

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It was an exciting and busy 24 hours at the National Zoo’s Conservation and Research Center in Front Royal, Va., last week as three births took place just hours apart. On the evening of July 9, a clouded leopard cub was born, followed by a Przewalski’s horse foal and a red panda cub.

The post Baby Boom of Endangered Species at Smithsonian’s National Zoo’s Conservation and Research Center appeared first on Smithsonian Insider.

In southeastern Greenland, two rivers of ice named Helheim and Kangerdlugssuaq flow in spurts and starts toward the coast. They are much like any other […]

The post Astrophysical Observatory scientists are monitoring the mysterious movements of glaciers appeared first on Smithsonian Insider.

The fossil teeth of a 15- to 18-million-year-old three-toed browsing horse, Anchitherium clarencei, were recently discovered by scientists from the Smithsonian Tropical Research Institute and the […]

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When songwriter Oscar Hammerstein penned the lyrics “fish gotta swim, birds gotta fly,” he clearly did not have the ratites in mind. Large flightless birds, the ratites include ostriches, emus, rheas and cassowaries, along with kiwis and several extinct species.

The post DNA evidence is rearranging the branches of the avian family tree appeared first on Smithsonian Insider.

A new Smithsonian study that examines 10 million years of the evolution of tiny coral-like organisms called cupuladriid bryzoans has revealed that some species of this organism lingered on earth for more than one million years after the event that ultimately caused their extinction: the rising of the Isthmus of Panama.

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Already under siege from overfishing, disease and poor water quality, the oyster population in the Chesapeake Bay today stands at 2 percent of what it was in colonial times. Now, new data show that rising acidity in the Bay will have a negative impact on oyster shells.

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New observations by the Smithsonian’s Submillimeter Array, a radio telescope atop Mauna Kea in Hawaii, are shedding light on planet formation. The array provides sharp views by combining eight antennas into the equivalent of a single, large telescope. It can resolve details as small as a dime seen from seven miles away.

The post Cosmic “baby photos” of distant solar systems lend insight as to how planets form appeared first on Smithsonian Insider.

A Smithsonian Institution biologist, working with the Natural History Unit of the British Broadcasting Corp., has discovered a new species of giant rat on a film-making expedition to a remote rainforest in New Guinea.

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Testing caterpillars’ taste buds is no simple task. Just like your local salad bar, plants in the wild come in different shapes, textures and flavors. Herbivores rely on each of these cues to tell them what to eat. Deciphering this code is Lind’s task. He’s examining 40 different plant species – half invasive, half native.

The post Salad science: Coaxing caterpillars to reveal the secrets of their leafy desires appeared first on Smithsonian Insider.

The giant squid was collected during a 60-day scientific study in which NOAA scientists were studying the availability and diversity of sperm whale prey. The squid was caught in a trawl net pulled behind a research vessel at a depth of more than 1,500 feet.

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Scientists from the Smithsonian Migratory Bird Center at the National Zoo have taken blood samples from thousands of birds and mosquitoes in an effort to track the progress of the West Nile Virus in the eastern United States. Come along in this video as Smithsonian scientists net birds living in downtown Washington, D.C., extract small amounts of blood, and then release them back into the "wild."

The post Video: Common birds in Washington, D.C. are helping Smithsonian scientists track intensity of the West Nile Virus appeared first on Smithsonian Insider.

A major new exhibition hall dedicated to the discovery and understanding of human origins will open next year at the Smithsonian's National Museum of Natural History: The David H. Koch Hall of Human Origins

The post Hall of Human Origins to open at Smithsonian’s Natural History Museum, March 17, 2010 appeared first on Smithsonian Insider.

Native to Africa and Madagascar, females of the species have a body length of 1.5 inches and a leg span of 4 to 5 inches. Males are tiny in comparison.

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The National Zoo has been awarded a grant from the U.S. Fish and Wildlife Service to establish a captive population of the Virginia big-eared bat at the National Zoo’s Conservation & Research Center near Front Royal, Va. Only 15,000 Virginia big-eared bats remain living in caves in West Virginia, Virginia, Kentucky and North Carolina, and these are threatened by the white-nose syndrome.

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Invasive species, contaminants, excessive nutrient's and sediment are just some of the many factors threatening sensitive wetlands and seagrass beds.

The post Smithsonian to lead study on degradation of nearshore coastal habitats of the Chesapeake appeared first on Smithsonian Insider.

Nearly 100 years ago, scientists detected the first signs of cosmic rays—subatomic particles (mostly protons) that zip through space at nearly the speed of light. […]

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In a series of ongoing experiments on Barro Colorado Island in the Panama Canal, Kays and other researchers are using camera traps, radio collars and palm nuts with tracking transmitters attached to them to take a closer look at the nut-hoarding strategies of the agouti.

The post Camera traps & radio collars reveal hoarding strategies of the South American agouti appeared first on Smithsonian Insider.

Dennis W. Kelly has been named director of the Smithsonian’s National Zoo in Washington, D.C., effective Feb. 15, 2010.

The post Dennis Kelly Named Director of the Smithsonian’s National Zoo appeared first on Smithsonian Insider.

Recently, researchers from Boston University and the Smithsonian Tropical Research Institute in Panama have been taking a closer look at the vibrations that red-eyed treefrog embryos use as cues to trigger early hatching. They discovered that treefrog embryos can evaluate different features of vibrations.

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